Analisis of Salmonella isolated from food confiscated from non-EU flights passengers at Bilbao airport (Spain)

TORMES version 1.0

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• Samples description

• Assembly analysis

• MLST

• Serotyping

• Pangenome analysis

• Antibiotic resistance

• Virulence genes

• Plasmid replicons

• Citation

Samples description

Samples	Source	Country of origin	Isolation date
MS0495	Cheese	Georgia	03/08/2012
MS0496	Cheese	Bolivia	03/08/2012
MS0497	Cheese	Moldova	30/08/2012
MS0498	Meat	Peru	30/05/2012
MS0499	Cheese	Peru	30/05/2012
MS0500	Poultry	Eq. Guinea	24/08/2012
MS0501	Poultry	Eq. Guinea	24/08/2012
MS0502	Meat	Bolivia	16/02/2013
MS0503	Meat	Bolivia	16/02/2013
MS0504	Cheese	Bolivia	16/02/2013

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Assembly analysis

Field	Description
Sample	Name of the sample
Reads	Total number of reads after quality filtering
AvgReadLen	Average read length after quality filtering
Contigs	Number of contigs of the draft genome (>200bp)
GenomeLength	Length (bp) of the draft genome
AvgContigLen	Average contig length (>200bp)
N50	“Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly” (Miller et al., 2010)
GC	GC content (%) of the draft genome
Depth	Number of times each nucleotide position in the draft genome has a read that align to that position
Specie	Specie identification by Kraken
PercentID	Number of reads (%) assigned as that specie by Kraken

Contig ordering was performed against file: ../Salmonella_references/S_enterica_CT_02021853.fasta

Sample	Reads	AvgReadLen	Contigs	GenomeLength	AvgContigLen	N50	GC	Depth	Specie	PercentID
MS0495	587544	259	41	4650624	640249	308791	52.26	32X	Salmonella enterica	98.25
MS0496	888038	254	107	4763977	336019	136467	52.15	47X	Salmonella enterica	94.20
MS0497	622536	257	91	4643658	438202	128141	52.29	34X	Salmonella enterica	98.25
MS0498	673312	260	154	4757288	225116	83927	52.17	36X	Salmonella enterica	94.55
MS0499	828090	247	115	4760115	414408	99676	52.16	42X	Salmonella enterica	94.54
MS0500	793160	257	64	4652143	439190	174151	52.15	43X	Salmonella enterica	97.47
MS0501	666626	261	178	4560864	209922	65339	52.19	38X	Salmonella enterica	98.87
MS0502	692768	256	73	4637517	558286	204883	52.17	38X	Salmonella enterica	97.83
MS0503	620020	257	74	4634553	408239	198288	52.17	34X	Salmonella enterica	97.96
MS0504	542482	262	188	4709098	206809	52159	52.29	30X	Salmonella enterica	97.80

Select the parameter

Number of reads

## Warning: package 'bindrcpp' was built under R version 3.4.4

Average number of reads per sample = 691458

Average read length

Average read length per sample = 257 bp

Number of contigs

Average number of contigs per sample = 108

Draft genome length

Average draft genome length per sample = 4676984 bp

Average contig length

Average contig length per sample = 387644 bp

N50

Average N50 per sample = 145182 bp

GC content

Average GC content per sample = 52.2%

Sequencing depth

Average sequencing depth = 37.4X

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MLST

Further details can be found in mlst web page.

Symbol	Meaning
~	novel full length allele similar to match
?	partial match to known allele
-	allele missing

	Scheme	ST	1	2	3	4	5	6	7
MS0495	senterica	4	aroC(43)	dnaN(41)	hemD(16)	hisD(13)	purE(34)	sucA(13)	thrA(4)
MS0496	senterica	279	aroC(62)	dnaN(95)	hemD(54)	hisD(96)	purE(100)	sucA(9)	thrA(100)
MS0497	senterica	4	aroC(43)	dnaN(41)	hemD(16)	hisD(13)	purE(34)	sucA(13)	thrA(4)
MS0498	senterica	279	aroC(62)	dnaN(95)	hemD(54)	hisD(96)	purE(100)	sucA(9)	thrA(100)
MS0499	senterica	279	aroC(62)	dnaN(95)	hemD(54)	hisD(96)	purE(100)	sucA(9)	thrA(100)
MS0500	senterica	11	aroC(5)	dnaN(2)	hemD(3)	hisD(7)	purE(6)	sucA(6)	thrA(11)
MS0501	senterica	23	aroC(13)	dnaN(11)	hemD(16)	hisD(15)	purE(12)	sucA(15)	thrA(4)
MS0502	senterica	64	aroC(10)	dnaN(14)	hemD(15)	hisD(31)	purE(25)	sucA(20)	thrA(33)
MS0503	senterica	64	aroC(10)	dnaN(14)	hemD(15)	hisD(31)	purE(25)	sucA(20)	thrA(33)
MS0504	senterica	45	aroC(10)	dnaN(7)	hemD(21)	hisD(14)	purE(15)	sucA(12)	thrA(12)

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Serotyping

Sample	Subspecie	Serovar	Serogroup	H1	H2	Quality Control
MS0495	enterica	Montevideo	C1	g,m,[p],s	-	PASS
MS0496	enterica	I 4,[5],12:d:-	B	d	-	PASS
MS0497	enterica	Montevideo	C1	g,m,[p],s	-	PASS
MS0498	enterica	I 4,[5],12:d:-	B	d	-	PASS
MS0499	enterica	I 4,[5],12:d:-	B	d	-	PASS
MS0500	enterica	Enteritidis	D1	g,m	-	PASS
MS0501	enterica	Oranienburg	C1	m,t	-	PASS
MS0502	enterica	Anatum	E1	e,h	1,6	PASS
MS0503	enterica	Anatum	E1	e,h	1,6	PASS
MS0504	enterica	Newport	C2-C3	e,h	1,2	PASS

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Pangenome analysis

Pangenome genes summary

Genes	Description	Number
Core genes	(99% <= strains <= 100%)	3602
Soft core genes	(95% <= strains < 99%)	0
Shell genes	(15% <= strains < 95%)	1607
Cloud genes	(0% <= strains < 15%)	614
Total genes	(0% <= strains <= 100%)	5823

Pangenome genes presence-absence

Pangenome tree representation

Rectangular (phylogram)

Circular (phylogram)

Rectangular (cladogram)

Circular (cladogram)

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Antibiotic resistance

The search of antibiotic resistance genes was performed by screening of the draft genome against Resfinder (E. Zankari et al., 2012), CARD (A.G. McArthur et al., 2013) and ARG-ANNOT (S.K. Gupta et al., 2014) databases by using Abricate. Any hit with coverage and/or identity below 90% was removed.

Field	Description
Contig	Contig name where the gene was found
Start	Start position of the gene within the contig
End	End position of the gene within the contig
Gene	Antibiotic resistance gene
Gaps	Gaps in subject (draft genome) and query (antibiotic resistance genes)
Coverage	Proportion (%) of the gene covered
Identity	Proportion (%) of exact nucleotide matches
Accession	Accesion number of the antibiotic resistance gene
Product	Antibiotic resistance gene product

Select the samples and the database

MS0495

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_586740 cov_13.4114	170029	170466	aac(6’)-Iaa_1	0/0	100	97.9	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_586740 cov_13.4114	170028	170466	AAC(6’)-Iy	0/0	100	98.4	AF144880:3542-3980	AAC(6’)-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6’)-Iy gene was placed under the control of the upstream nmpC promoter.
NODE_4 length_313823 cov_16.4377	103427	103892	golS	0/0	100	99.4	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_4 length_313823 cov_16.4377	99623	100829	mdsA	0/0	100	98.4	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_4 length_313823 cov_16.4377	96459	99627	mdsB	0/0	100	99.0	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_4 length_313823 cov_16.4377	94985	96443	mdsC	0/0	100	97.9	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_9 length_225727 cov_13.6267	5582	7006	mdtK	0/0	100	98.6	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_9 length_225727 cov_13.6267	53530	54253	sdiA	0/0	100	98.5	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_586740 cov_13.4114	170029	170466	(AGly)Aac6-Iy	0/0	100	98.4	AF144880:3452-3979	(AGly)Aac6-Iy

MS0496

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_311067 cov_18.109	12513	12950	aac(6’)-Iaa_1	0/0	100	99.3	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_311067 cov_18.109	12512	12950	AAC(6’)-Iaa	0/0	100	99.3	NC_003197:1707358-1707796	AAC(6’)-Iaa is a chromosomal-encoded aminoglycoside acetyltransferase in S. typhimurium
NODE_10 length_157979 cov_23.6405	89747	90212	golS	0/0	100	99.4	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_10 length_157979 cov_23.6405	92809	94015	mdsA	0/0	100	99.3	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_10 length_157979 cov_23.6405	94011	97179	mdsB	0/0	100	98.9	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_10 length_157979 cov_23.6405	97195	98653	mdsC	0/0	100	98.6	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_5 length_238301 cov_19.1003	210842	212266	mdtK	0/0	100	99.0	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_11 length_136467 cov_17.9726	36340	37063	sdiA	0/0	100	98.5	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_311067 cov_18.109	12513	12950	(AGly)Aac6-Iaa	0/0	100	99.3	NC_003197:1707358-1707795	(AGly)Aac6-Iaa

MS0497

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_12 length_115250 cov_14.1838	52434	52871	aac(6’)-Iaa_1	0/0	100	97.9	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_12 length_115250 cov_14.1838	52434	52872	AAC(6’)-Iy	0/0	100	98.4	AF144880:3542-3980	AAC(6’)-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6’)-Iy gene was placed under the control of the upstream nmpC promoter.
NODE_23 length_64776 cov_17.0389	22287	22752	golS	0/0	100	99.4	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_23 length_64776 cov_17.0389	25350	26556	mdsA	0/0	100	98.4	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_23 length_64776 cov_17.0389	26552	29720	mdsB	0/0	100	99.0	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_23 length_64776 cov_17.0389	29736	31194	mdsC	0/0	100	97.9	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_51 length_17197 cov_16.0824	10192	11616	mdtK	0/0	100	98.6	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_13 length_112638 cov_15.7484	75571	76294	sdiA	0/0	100	98.5	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_12 length_115250 cov_14.1838	52434	52871	(AGly)Aac6-Iy	0/0	100	98.4	AF144880:3452-3979	(AGly)Aac6-Iy

MS0498

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_27 length_65470 cov_13.5488	52426	52863	aac(6’)-Iaa_1	0/0	100	99.3	NC_003197	aac(6’)-Iaa_1
NODE_95 length_2826 cov_1538.31	1092	1736	qnrB19_1	0/0	100	100.0	EU432277	qnrB19_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_27 length_65470 cov_13.5488	52426	52864	AAC(6’)-Iaa	0/0	100	99.3	NC_003197:1707358-1707796	AAC(6’)-Iaa is a chromosomal-encoded aminoglycoside acetyltransferase in S. typhimurium
NODE_4 length_153648 cov_17.5344	89707	90172	golS	0/0	100	99.4	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_4 length_153648 cov_17.5344	92769	93975	mdsA	0/0	100	99.3	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_4 length_153648 cov_17.5344	93971	97139	mdsB	0/0	100	98.9	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_4 length_153648 cov_17.5344	97155	98613	mdsC	0/0	100	98.6	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_15 length_93408 cov_15.3063	20276	21700	mdtK	0/0	100	99.0	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_95 length_2826 cov_1538.31	1056	1736	QnrB5	0/0	100	99.1	DQ303919:1-682	QnrB5 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica
NODE_9 length_115205 cov_14.3578	36324	37047	sdiA	0/0	100	98.5	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_27 length_65470 cov_13.5488	52426	52863	(AGly)Aac6-Iaa	0/0	100	99.3	NC_003197:1707358-1707795	(AGly)Aac6-Iaa
NODE_95 length_2826 cov_1538.31	1056	1736	(Flq)QnrB5	0/0	100	99.1	DQ303919:1-681	(Flq)QnrB5

MS0499

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_5 length_224057 cov_15.0684	87858	88295	aac(6’)-Iaa_1	0/0	100	99.3	NC_003197	aac(6’)-Iaa_1
NODE_71 length_2826 cov_1536.91	1092	1736	qnrB19_1	0/0	100	100.0	EU432277	qnrB19_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_5 length_224057 cov_15.0684	87857	88295	AAC(6’)-Iaa	0/0	100	99.3	NC_003197:1707358-1707796	AAC(6’)-Iaa is a chromosomal-encoded aminoglycoside acetyltransferase in S. typhimurium
NODE_2 length_403701 cov_18.9992	338806	339271	golS	0/0	100	99.4	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_2 length_403701 cov_18.9992	341868	343074	mdsA	0/0	100	99.3	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_2 length_403701 cov_18.9992	343070	346238	mdsB	0/0	100	98.9	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_2 length_403701 cov_18.9992	346254	347712	mdsC	0/0	100	98.6	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_4 length_236778 cov_16.7821	209399	210823	mdtK	0/0	100	99.0	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_71 length_2826 cov_1536.91	1056	1736	QnrB5	0/0	100	99.1	DQ303919:1-682	QnrB5 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica
NODE_7 length_162718 cov_15.3676	147588	148311	sdiA	0/0	100	98.5	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_5 length_224057 cov_15.0684	87858	88295	(AGly)Aac6-Iaa	0/0	100	99.3	NC_003197:1707358-1707795	(AGly)Aac6-Iaa
NODE_71 length_2826 cov_1536.91	1056	1736	(Flq)QnrB5	0/0	100	99.1	DQ303919:1-681	(Flq)QnrB5

MS0500

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_343106 cov_18.4156	51079	51516	aac(6’)-Iaa_1	0/0	100	96.3	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_343106 cov_18.4156	51078	51516	AAC(6’)-Iy	0/0	100	96.8	AF144880:3542-3980	AAC(6’)-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6’)-Iy gene was placed under the control of the upstream nmpC promoter.
NODE_1 length_439190 cov_21.4436	80973	81438	golS	0/0	100	99.6	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_1 length_439190 cov_21.4436	77170	78376	mdsA	0/0	100	98.8	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_1 length_439190 cov_21.4436	74006	77174	mdsB	0/0	100	99.5	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_1 length_439190 cov_21.4436	72532	73990	mdsC	0/0	100	98.3	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_22 length_65495 cov_19.9673	18811	20235	mdtK	0/0	100	98.8	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_11 length_170699 cov_18.423	128452	129175	sdiA	0/0	100	99.3	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_343106 cov_18.4156	51079	51516	(AGly)Aac6-Iy	0/0	100	96.8	AF144880:3452-3979	(AGly)Aac6-Iy

MS0501

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_50 length_31448 cov_14.8458	15446	15883	aac(6’)-Iaa_1	0/0	100	97.9	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_50 length_31448 cov_14.8458	15446	15884	AAC(6’)-Iy	0/0	100	98.4	AF144880:3542-3980	AAC(6’)-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6’)-Iy gene was placed under the control of the upstream nmpC promoter.
NODE_19 length_66119 cov_19.6698	42035	42500	golS	0/0	100	99.4	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_19 length_66119 cov_19.6698	38232	39438	mdsA	0/0	100	98.8	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_19 length_66119 cov_19.6698	35068	38236	mdsB	0/0	100	99.0	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_19 length_66119 cov_19.6698	33594	35052	mdsC	0/0	100	98.4	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_79 length_14440 cov_16.116	5595	7019	mdtK	0/0	100	98.7	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_27 length_54018 cov_17.5413	36185	36908	sdiA	0/0	100	98.8	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_50 length_31448 cov_14.8458	15446	15883	(AGly)Aac6-Iy	0/0	100	98.4	AF144880:3452-3979	(AGly)Aac6-Iy

MS0502

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_1 length_558286 cov_14.6997	474259	474696	aac(6’)-Iaa_1	0/0	100	99.1	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_1 length_558286 cov_14.6997	474259	474697	AAC(6’)-Iy	0/0	100	99.5	AF144880:3542-3980	AAC(6’)-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6’)-Iy gene was placed under the control of the upstream nmpC promoter.
NODE_8 length_198416 cov_20.1779	89718	90183	golS	0/0	100	98.9	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_8 length_198416 cov_20.1779	92780	93986	mdsA	0/0	100	98.7	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_8 length_198416 cov_20.1779	93982	97150	mdsB	0/0	100	99.1	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_8 length_198416 cov_20.1779	97166	98624	mdsC	0/0	100	98.6	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_2 length_395533 cov_15.2345	72990	74414	mdtK	0/0	100	99.1	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_2 length_395533 cov_15.2345	142493	143216	sdiA	0/0	100	99.0	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_1 length_558286 cov_14.6997	474259	474696	(AGly)Aac6-Iy	0/0	100	99.5	AF144880:3452-3979	(AGly)Aac6-Iy

MS0503

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_403085 cov_13.5055	175360	175797	aac(6’)-Iaa_1	0/0	100	99.1	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_403085 cov_13.5055	175359	175797	AAC(6’)-Iy	0/0	100	99.5	AF144880:3542-3980	AAC(6’)-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6’)-Iy gene was placed under the control of the upstream nmpC promoter.
NODE_8 length_198288 cov_17.7731	108121	108586	golS	0/0	100	98.9	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_8 length_198288 cov_17.7731	104318	105524	mdsA	0/0	100	98.7	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_8 length_198288 cov_17.7731	101154	104322	mdsB	0/0	100	99.1	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_8 length_198288 cov_17.7731	99680	101138	mdsC	0/0	100	98.6	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_27 length_36756 cov_14.8978	10551	11975	mdtK	0/0	100	99.1	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_10 length_196382 cov_14.5915	36337	37060	sdiA	0/0	100	99.0	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_403085 cov_13.5055	175360	175797	(AGly)Aac6-Iy	0/0	100	99.5	AF144880:3452-3979	(AGly)Aac6-Iy

MS0504

Resfinder

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_62 length_27019 cov_12.7387	14103	14540	aac(6’)-Iaa_1	0/0	100	99.5	NC_003197	aac(6’)-Iaa_1

CARD

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_62 length_27019 cov_12.7387	14103	14541	AAC(6’)-Iy	0/0	100	100.0	AF144880:3542-3980	AAC(6’)-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6’)-Iy gene was placed under the control of the upstream nmpC promoter.
NODE_32 length_46760 cov_15.3308	22637	23102	golS	0/0	100	99.4	NC_003197:400860-401325	GolS is a regulator activated by the presence of gold and promotes the expression of the MdsABC efflux pump.
NODE_32 length_46760 cov_15.3308	18834	20040	mdsA	0/0	100	98.9	NC_003197:397057-398263	MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.
NODE_32 length_46760 cov_15.3308	15670	18838	mdsB	0/0	100	99.6	NC_003197:393893-397061	MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC.
NODE_32 length_46760 cov_15.3308	14196	15654	mdsC	0/0	100	99.5	NC_003197:392419-393877	MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.
NODE_36 length_43603 cov_13.8252	16229	17653	mdtK	0/0	100	99.0	CP014358.1:2161326-2162751	A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine.
NODE_35 length_43892 cov_14.2588	26097	26820	sdiA	0/0	100	98.8	NC_003197:2039658-2040381	SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it’s expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB

ARG-ANNOT

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_62 length_27019 cov_12.7387	14103	14540	(AGly)Aac6-Iy	0/0	100	100	AF144880:3452-3979	(AGly)Aac6-Iy

Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample.

Select the database:

Resfinder

CARD

ARG-ANNOT

Antibiotic resistance genes (ResFinder) count

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Antibiotic resistance due to point mutations

Select the sample

MS0495

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0496

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0497

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0498

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0499

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0500

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0501

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0502

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0503

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

MS0504

## [1] "No known mutations from PointFinder database were found. For unknown mutations check point_mutations directory"

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Virulence genes

The search of virulence genes was performed by screening of the draft genome against Virulence Factors Data Base (VFDB, L. Chen et al., 2005) by using Abricate. Any hit with coverage and/or identity below 90% was removed. To see description of each field, click here.

Select the sample

MS0495

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_1 length_640249 cov_18.3026	372994	373536	bcfA	0/0	100.0	98.5	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_640249 cov_18.3026	373637	374323	bcfB	0/0	100.0	99.4	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_640249 cov_18.3026	374328	376948	bcfC	1/1	100.0	98.4	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_640249 cov_18.3026	376949	377956	bcfD	0/0	100.0	97.7	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_640249 cov_18.3026	377957	378502	bcfE	0/0	100.0	98.0	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_640249 cov_18.3026	378518	379036	bcfF	0/0	100.0	97.9	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_640249 cov_18.3026	379002	379733	bcfG	0/0	100.0	97.8	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	546503	547312	cdtB	0/0	100.0	99.9	NP_456275	(cdtB) cytolethal distending toxin B [CdtB (VF0407)] [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
NODE_10 length_155157 cov_14.382	70219	70674	csgA	0/0	100.0	98.9	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	70716	71171	csgB	0/0	100.0	99.3	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	69831	70157	csgC	0/0	100.0	99.7	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	71926	72576	csgD	0/0	100.0	99.2	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	72581	72976	csgE	0/0	100.0	99.5	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	73003	73419	csgF	0/0	100.0	99.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	73446	74279	csgG	0/0	100.0	99.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_313823 cov_16.4377	303273	303965	fimC	0/0	100.0	98.7	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_313823 cov_16.4377	303996	306608	fimD	0/0	100.0	98.8	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_313823 cov_16.4377	307640	308157	fimF	0/0	99.8	98.5	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_313823 cov_16.4377	306623	307630	fimH	0/0	100.0	98.4	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_313823 cov_16.4377	302696	303229	fimI	0/0	100.0	98.1	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	207694	209751	invA	0/0	100.0	99.1	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	207263	207670	invB	0/0	100.0	99.3	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	205971	207266	invC	0/0	100.0	99.1	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	209776	210894	invE	0/0	100.0	99.2	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	212576	213226	invF	0/0	100.0	98.8	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	210891	212579	invG	0/0	100.0	98.9	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	213683	214126	invH	0/0	100.0	98.9	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	205550	205993	invI	0/0	100.0	99.5	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	204540	205550	invJ	0/0	100.0	99.4	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_95766 cov_20.1625	44828	47554	mgtB	0/0	100.0	98.8	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_95766 cov_20.1625	47773	48468	mgtC	0/0	100.0	98.4	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	99434	100330	mig-14	0/0	100.0	97.2	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_95766 cov_20.1625	38121	40973	misL	1/15	99.5	97.7	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	183729	184328	orgA	0/0	100.0	99.2	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	183082	183772	orgB	1/10	100.0	97.8	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	182633	183085	orgC	0/0	100.0	98.5	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	124683	125558	pipB	0/0	100.0	98.9	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	185646	186824	prgH	0/0	100.0	99.2	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	185379	185621	prgI	0/0	100.0	100.0	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	185055	185360	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	184300	185058	prgK	0/0	100.0	99.6	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_243417 cov_15.3434	105454	112764	ratB	5/7	100.0	91.0	NP_461449	(ratB) putative outer membrane protein [RatB (VF0399)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	200192	200689	sicA	0/0	100.0	99.4	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	192992	193384	sicP	0/0	100.0	99.2	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	573196	574206	sifA	0/0	100.0	96.2	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	184693	185643	sifB	0/0	100.0	95.6	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_243417 cov_15.3434	96387	98579	sinH	0/0	100.0	95.9	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	193982	196039	sipA/sspA	0/0	100.0	98.3	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	198408	200189	sipB/sspB	0/0	100.0	99.5	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	197151	198380	sipC/sspC	0/0	100.0	99.4	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	196058	197080	sipD	3/11	99.0	90.4	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_260571 cov_14.4785	77992	80259	slrP	2/30	98.7	94.7	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_126356 cov_13.7393	78455	80803	sopA	0/0	100.0	97.4	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_155157 cov_14.382	122091	123776	sopB/sigD	0/0	100.0	98.4	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	256965	257918	sopD	0/0	100.0	97.9	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_260571 cov_14.4785	217318	218277	sopD2	0/0	100.0	93.2	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_225727 cov_13.6267	143223	143945	sopE2	0/0	100.0	97.0	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	203629	204540	spaO	0/0	100.0	99.5	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	202965	203639	spaP	0/0	100.0	98.8	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	202679	202939	spaQ	0/0	100.0	99.6	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	201884	202675	spaR	0/0	100.0	99.0	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	200827	201897	spaS	0/0	100.0	99.2	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	402072	402473	spiC/ssaB	0/0	100.0	99.2	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_551600 cov_18.0739	191374	193005	sptP	0/0	100.0	97.5	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	400577	402070	ssaC	0/0	100.0	98.5	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	399385	400596	ssaD	0/0	100.0	98.6	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	399135	399377	ssaE	0/0	100.0	98.8	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	392720	392935	ssaG	0/0	100.0	100.0	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	392452	392679	ssaH	0/0	100.0	99.6	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	392192	392440	ssaI	0/0	100.0	98.0	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	391446	392195	ssaJ	0/0	100.0	98.1	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	390209	390883	ssaK	0/0	100.0	98.8	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	389227	390243	ssaL	0/0	100.0	98.9	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	388801	389169	ssaM	0/0	100.0	97.3	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	385474	386781	ssaN	1/6	100.0	98.5	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	385094	385471	ssaO	0/0	100.0	98.9	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	384739	385113	ssaP	0/0	100.0	100.0	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	383790	384758	ssaQ	0/0	100.0	98.3	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	383075	383722	ssaR	0/0	100.0	98.9	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	382812	383078	ssaS	0/0	100.0	99.6	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	382032	382811	ssaT	0/0	100.0	97.6	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	380977	382035	ssaU	0/0	100.0	98.2	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	386771	388816	ssaV	0/0	100.0	98.9	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	397478	397951	sscA	0/0	100.0	97.3	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	394513	394947	sscB	0/0	100.0	99.5	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	398545	398871	sseA	0/0	100.0	99.4	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	397948	398538	sseB	0/0	100.0	97.5	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	396021	397475	sseC	0/0	100.0	97.2	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	395418	396005	sseD	0/0	100.0	96.8	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	394999	395415	sseE	0/0	100.0	99.3	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	393715	394497	sseF	0/0	100.0	98.1	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	393029	393718	sseG	0/0	100.0	97.7	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	155304	156530	sseJ	0/0	100.0	96.7	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_33132 cov_19.4242	13694	14704	sseK1	0/0	100.0	98.9	NP_463026	(sseK1) type III secretion system effector SseK1 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_154126 cov_14.7001	111528	112481	sseL	0/0	100.0	96.5	NP_461229	(sseL) type III secretion system effector SseL deubiquitinase [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	207660	208292	steA	0/0	100.0	94.2	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	157801	158202	steB	0/0	100.0	95.5	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_586740 cov_13.4114	77837	79210	steC	0/0	100.0	94.9	NP_460656	(steC) type III secretion system effector SteC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

MS0496

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_1 length_336019 cov_22.7038	187964	188872	avrA	0/0	100.0	99.5	NP_461786	(avrA) type III secretion system effector AvrA acetyltransferease [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_135220 cov_24.871	8084	8626	bcfA	0/0	100.0	99.5	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_135220 cov_24.871	7297	7983	bcfB	0/0	100.0	99.6	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_135220 cov_24.871	4671	7292	bcfC	0/0	100.0	98.9	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_135220 cov_24.871	3663	4670	bcfD	0/0	100.0	98.6	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_135220 cov_24.871	3117	3662	bcfE	0/0	100.0	98.2	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_135220 cov_24.871	2583	3101	bcfF	0/0	100.0	98.1	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_135220 cov_24.871	1886	2617	bcfG	0/0	100.0	98.4	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	180763	181218	csgA	0/0	100.0	98.7	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	181260	181715	csgB	0/0	100.0	100.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	180375	180701	csgC	0/0	100.0	100.0	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	182470	183120	csgD	0/0	100.0	99.2	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	183125	183520	csgE	0/0	100.0	100.0	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	183547	183963	csgF	0/0	100.0	99.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	183990	184823	csgG	0/0	100.0	99.6	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_249088 cov_21.088	114373	115065	fimC	0/0	100.0	98.7	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_249088 cov_21.088	115096	117708	fimD	0/0	100.0	98.9	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_249088 cov_21.088	118740	119258	fimF	0/0	100.0	98.3	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_249088 cov_21.088	117723	118730	fimH	0/0	100.0	97.9	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_249088 cov_21.088	113796	114329	fimI	0/0	100.0	99.1	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	158303	160360	invA	0/0	100.0	99.6	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	160384	160791	invB	0/0	100.0	99.3	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	160788	162083	invC	0/0	100.0	99.4	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	157160	158278	invE	0/0	100.0	99.7	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	154828	155478	invF	0/0	100.0	99.7	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	155475	157163	invG	0/0	100.0	99.5	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	153927	154370	invH	0/0	100.0	99.3	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	162061	162504	invI	0/0	100.0	99.3	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	162504	163514	invJ	0/0	100.0	99.3	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_221558 cov_23.7331	220921	221457	lpfA	0/0	100.0	96.8	NP_462541	(lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_221558 cov_23.7331	220139	220837	lpfB	0/0	100.0	98.7	NP_462540	(lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_221558 cov_23.7331	217588	220116	lpfC	0/0	100.0	98.5	NP_462539	(lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_221558 cov_23.7331	215973	216500	lpfE	0/0	100.0	99.2	NP_462537	(lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_107805 cov_25.9279	42677	45403	mgtB	0/0	100.0	98.8	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_107805 cov_25.9279	41762	42457	mgtC	0/0	100.0	99.0	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	268365	269261	mig-14	0/0	100.0	97.7	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_107805 cov_25.9279	49316	52183	misL	3/30	99.5	97.4	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	183735	184334	orgA	0/0	100.0	99.5	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	184291	184981	orgB	1/10	100.0	97.5	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	184978	185430	orgC	0/0	100.0	98.0	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_128252 cov_19.1426	21371	22246	pipB	0/0	100.0	98.7	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	271002	272054	pipB2	0/0	100.0	93.9	NP_461706	(pipB2) type III secretion system effector PipB3 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	181239	182417	prgH	0/0	100.0	99.3	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	182442	182684	prgI	0/0	100.0	98.8	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	182703	183008	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	183005	183763	prgK	0/0	100.0	99.5	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	167365	167862	sicA	0/0	100.0	99.4	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	174679	175071	sicP	0/0	100.0	99.5	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_238301 cov_19.1003	101991	103001	sifA	0/0	100.0	96.1	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	27176	28126	sifB	0/0	100.0	95.7	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_242135 cov_21.4062	193	2385	sinH	0/0	100.0	97.6	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	172024	174081	sipA/sspA	0/0	100.0	99.2	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	167865	169646	sipB/sspB	0/0	100.0	99.5	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	169674	170903	sipC/sspC	0/0	100.0	99.7	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	170974	172005	sipD	0/0	100.0	98.7	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_59659 cov_19.1353	22818	25085	slrP	1/30	98.7	95.3	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_31 length_50067 cov_19.6621	22900	25248	sopA	0/0	100.0	98.1	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_128252 cov_19.1426	18347	20032	sopB/sigD	0/0	100.0	97.6	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	109757	110710	sopD	0/0	100.0	98.2	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_128252 cov_19.1426	97838	98797	sopD2	0/0	100.0	92.6	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_136467 cov_17.9726	115585	116307	sopE2	0/0	100.0	96.7	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	163514	164425	spaO	0/0	100.0	99.5	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	164415	165089	spaP	0/0	100.0	99.4	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	165115	165375	spaQ	0/0	100.0	99.2	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	165379	166170	spaR	0/0	100.0	99.6	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	166157	167227	spaS	0/0	100.0	99.9	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	242392	242793	spiC/ssaB	0/0	100.0	99.8	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_336019 cov_22.7038	175058	176689	sptP	0/0	100.0	98.4	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	240897	242390	ssaC	0/0	100.0	98.7	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	239705	240916	ssaD	0/0	100.0	98.7	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	239455	239697	ssaE	0/0	100.0	98.8	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	233042	233257	ssaG	0/0	100.0	99.1	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	232774	233001	ssaH	0/0	100.0	99.1	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	232514	232762	ssaI	0/0	100.0	98.4	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	231768	232517	ssaJ	0/0	100.0	98.5	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	230531	231205	ssaK	0/0	100.0	98.8	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	229549	230565	ssaL	0/0	100.0	99.0	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	229123	229491	ssaM	0/0	100.0	98.6	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	225802	227103	ssaN	0/0	100.0	98.5	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	225422	225799	ssaO	0/0	100.0	99.2	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	225067	225441	ssaP	0/0	100.0	98.7	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	224118	225086	ssaQ	0/0	100.0	98.6	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	223403	224050	ssaR	0/0	100.0	99.5	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	223140	223406	ssaS	0/0	100.0	100.0	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	222360	223139	ssaT	0/0	100.0	98.1	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	221305	222363	ssaU	0/0	100.0	97.7	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	227093	229138	ssaV	0/0	100.0	99.1	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	237799	238272	sscA	0/0	100.0	97.7	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	234834	235268	sscB	0/0	100.0	99.8	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	238866	239192	sseA	0/0	100.0	98.8	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	238269	238859	sseB	0/0	100.0	96.6	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	236342	237796	sseC	0/0	100.0	95.7	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	235739	236326	sseD	0/0	100.0	95.4	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	235320	235736	sseE	0/0	100.0	98.3	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	234036	234818	sseF	0/0	100.0	97.8	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	233350	234039	sseG	0/0	100.0	97.7	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_19 length_74778 cov_16.2228	479	1705	sseJ	0/0	100.0	96.4	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_112834 cov_20.1007	108117	109163	sseK2	0/0	100.0	99.1	NP_461081	(sseK2) type III secretion system effector SseK2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_74720 cov_19.205	41687	42640	sseL	0/0	100.0	94.8	NP_461229	(sseL) type III secretion system effector SseL deubiquitinase [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	50167	50799	steA	0/0	100.0	97.5	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_311067 cov_18.109	285	686	steB	0/0	100.0	97.0	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_19 length_74778 cov_16.2228	73422	74777	steC	0/0	98.7	95.8	NP_460656	(steC) type III secretion system effector SteC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

MS0497

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_2 length_347102 cov_19.3095	163600	164142	bcfA	0/0	100.0	98.5	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_347102 cov_19.3095	164243	164929	bcfB	0/0	100.0	99.4	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_347102 cov_19.3095	164934	167554	bcfC	1/1	100.0	98.4	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_347102 cov_19.3095	167555	168562	bcfD	0/0	100.0	97.7	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_347102 cov_19.3095	168563	169108	bcfE	0/0	100.0	98.0	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_347102 cov_19.3095	169124	169642	bcfF	0/0	100.0	97.9	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_347102 cov_19.3095	169608	170339	bcfG	0/0	100.0	97.8	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	218540	219349	cdtB	0/0	100.0	99.9	NP_456275	(cdtB) cytolethal distending toxin B [CdtB (VF0407)] [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
NODE_6 length_184030 cov_15.0903	99092	99547	csgA	0/0	100.0	98.9	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	99589	100044	csgB	0/0	100.0	99.3	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	98704	99030	csgC	0/0	100.0	99.7	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	100799	101449	csgD	0/0	100.0	99.2	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	101454	101849	csgE	0/0	100.0	99.5	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	101876	102292	csgF	0/0	100.0	99.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	102319	103152	csgG	0/0	100.0	99.3	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_28 length_57551 cov_15.8638	9363	10055	fimC	0/0	100.0	98.7	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_28 length_57551 cov_15.8638	6720	9332	fimD	0/0	100.0	98.8	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_28 length_57551 cov_15.8638	5171	5688	fimF	0/0	99.8	98.5	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_28 length_57551 cov_15.8638	5698	6705	fimH	0/0	100.0	98.4	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_28 length_57551 cov_15.8638	10099	10632	fimI	0/0	100.0	98.1	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	61127	63184	invA	0/0	100.0	99.1	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	63208	63615	invB	0/0	100.0	99.3	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	63612	64907	invC	0/0	100.0	99.1	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	59984	61102	invE	0/0	100.0	99.2	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	57652	58302	invF	0/0	100.0	98.8	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	58299	59987	invG	0/0	100.0	98.9	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	56752	57195	invH	0/0	100.0	98.9	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	64885	65328	invI	0/0	100.0	99.5	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	65328	66338	invJ	0/0	100.0	99.4	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_31 length_52834 cov_20.0808	1896	4622	mgtB	0/0	100.0	98.8	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_31 length_52834 cov_20.0808	4841	5536	mgtC	0/0	100.0	98.4	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	170548	171444	mig-14	0/0	100.0	97.2	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_36 length_38948 cov_20.2166	1847	4699	misL	1/15	99.5	97.7	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	86550	87149	orgA	0/0	100.0	99.2	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	87106	87796	orgB	1/10	100.0	97.8	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	87793	88245	orgC	0/0	100.0	98.5	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	153556	154431	pipB	0/0	100.0	98.9	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	84054	85232	prgH	0/0	100.0	99.2	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	85257	85499	prgI	0/0	100.0	100.0	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	85518	85823	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	85820	86578	prgK	0/0	100.0	99.6	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_24 length_63246 cov_15.6225	55531	62841	ratB	5/7	100.0	91.0	NP_461449	(ratB) putative outer membrane protein [RatB (VF0399)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	70189	70686	sicA	0/0	100.0	99.4	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	77494	77886	sicP	0/0	100.0	99.2	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	15304	16314	sifA	0/0	100.0	96.2	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_115250 cov_14.1838	37257	38207	sifB	0/0	100.0	95.6	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_24 length_63246 cov_15.6225	46464	48656	sinH	0/0	100.0	95.9	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	74839	76896	sipA/sspA	0/0	100.0	98.3	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	70689	72470	sipB/sspB	0/0	100.0	99.5	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	72498	73727	sipC/sspC	0/0	100.0	99.4	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	73798	74820	sipD	3/11	99.0	90.4	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_181425 cov_14.6212	48247	50514	slrP	2/30	98.7	94.7	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_22 length_65103 cov_15.8057	45554	47902	sopA	0/0	100.0	97.4	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_184030 cov_15.0903	150964	152649	sopB/sigD	0/0	100.0	98.4	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	12960	13913	sopD	0/0	100.0	97.9	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_55 length_10197 cov_16.046	3517	4476	sopD2	0/0	100.0	93.2	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_75 length_1199 cov_12.8787	405	1127	sopE2	0/0	100.0	97.0	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	66338	67249	spaO	0/0	100.0	99.5	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	67239	67913	spaP	0/0	100.0	98.8	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	67939	68199	spaQ	0/0	100.0	99.6	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	68203	68994	spaR	0/0	100.0	99.0	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	68981	70051	spaS	0/0	100.0	99.2	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	74109	74510	spiC/ssaB	0/0	100.0	99.2	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_188460 cov_18.4717	77873	79504	sptP	0/0	100.0	97.5	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	72614	74107	ssaC	0/0	100.0	98.5	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	71422	72633	ssaD	0/0	100.0	98.6	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	71172	71414	ssaE	0/0	100.0	98.8	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	64757	64972	ssaG	0/0	100.0	100.0	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	64489	64716	ssaH	0/0	100.0	99.6	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	64229	64477	ssaI	0/0	100.0	98.0	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	63483	64232	ssaJ	0/0	100.0	98.1	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	62246	62920	ssaK	0/0	100.0	98.8	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	61264	62280	ssaL	0/0	100.0	98.9	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	60838	61206	ssaM	0/0	100.0	97.3	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	57511	58818	ssaN	1/6	100.0	98.5	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	57131	57508	ssaO	0/0	100.0	98.9	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	56776	57150	ssaP	0/0	100.0	100.0	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	55827	56795	ssaQ	0/0	100.0	98.3	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	55112	55759	ssaR	0/0	100.0	98.9	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	54849	55115	ssaS	0/0	100.0	99.6	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	54069	54848	ssaT	0/0	100.0	97.6	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	53014	54072	ssaU	0/0	100.0	98.2	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	58808	60853	ssaV	0/0	100.0	98.9	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	69515	69988	sscA	0/0	100.0	97.3	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	66550	66984	sscB	0/0	100.0	99.5	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	70582	70908	sseA	0/0	100.0	99.4	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	69985	70575	sseB	0/0	100.0	97.5	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	68058	69512	sseC	0/0	100.0	97.2	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	67455	68042	sseD	0/0	100.0	96.8	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	67036	67452	sseE	0/0	100.0	99.3	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	65752	66534	sseF	0/0	100.0	98.1	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_224730 cov_14.9174	65066	65755	sseG	0/0	100.0	97.7	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_115250 cov_14.1838	66370	67596	sseJ	0/0	100.0	96.7	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_49 length_19293 cov_16.0062	141	1151	sseK1	0/0	100.0	98.9	NP_463026	(sseK1) type III secretion system effector SseK1 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_27 length_59399 cov_15.1793	43063	44016	sseL	0/0	100.0	96.5	NP_461229	(sseL) type III secretion system effector SseL deubiquitinase [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_115250 cov_14.1838	14608	15240	steA	0/0	100.0	94.2	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_115250 cov_14.1838	64698	65099	steB	0/0	100.0	95.5	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_41 length_29783 cov_13.6631	28376	29749	steC	0/0	100.0	94.9	NP_460656	(steC) type III secretion system effector SteC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

MS0498

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_28 length_65386 cov_17.6524	62216	63124	avrA	0/0	100.0	99.5	NP_461786	(avrA) type III secretion system effector AvrA acetyltransferease [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_40 length_38992 cov_17.2665	9987	10529	bcfA	0/0	100.0	99.5	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_40 length_38992 cov_17.2665	9200	9886	bcfB	0/0	100.0	99.6	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_40 length_38992 cov_17.2665	6574	9195	bcfC	0/0	100.0	98.9	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_40 length_38992 cov_17.2665	5566	6573	bcfD	0/0	100.0	98.6	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_40 length_38992 cov_17.2665	5020	5565	bcfE	0/0	100.0	98.2	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_40 length_38992 cov_17.2665	4486	5004	bcfF	0/0	100.0	98.1	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_40 length_38992 cov_17.2665	3789	4520	bcfG	0/0	100.0	98.4	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_97993 cov_15.5134	1063	1518	csgA	0/0	100.0	98.7	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_97993 cov_15.5134	566	1021	csgB	0/0	100.0	100.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_97993 cov_15.5134	1580	1906	csgC	0/0	100.0	100.0	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_84 length_8172 cov_16.6145	95	745	csgD	0/0	100.0	99.2	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_84 length_8172 cov_16.6145	750	1145	csgE	0/0	100.0	100.0	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_84 length_8172 cov_16.6145	1172	1588	csgF	0/0	100.0	99.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_84 length_8172 cov_16.6145	1615	2448	csgG	0/0	100.0	99.6	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_53 length_28857 cov_15.7158	22945	23637	fimC	0/0	100.0	98.7	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_53 length_28857 cov_15.7158	23668	26280	fimD	0/0	100.0	98.9	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_53 length_28857 cov_15.7158	27312	27830	fimF	0/0	100.0	98.3	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_53 length_28857 cov_15.7158	26295	27302	fimH	0/0	100.0	97.9	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_53 length_28857 cov_15.7158	22368	22901	fimI	0/0	100.0	99.1	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	25195	27252	invA	0/0	100.0	99.6	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	24764	25171	invB	0/0	100.0	99.3	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	23472	24767	invC	0/0	100.0	99.4	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	27277	28395	invE	0/0	100.0	99.7	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	30077	30727	invF	0/0	100.0	99.7	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	28392	30080	invG	0/0	100.0	99.5	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	31185	31628	invH	0/0	100.0	99.3	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	23051	23494	invI	0/0	100.0	99.3	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	22041	23051	invJ	0/0	100.0	99.3	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_221410 cov_19.5443	86	622	lpfA	0/0	100.0	96.8	NP_462541	(lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_221410 cov_19.5443	706	1404	lpfB	0/0	100.0	98.7	NP_462540	(lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_221410 cov_19.5443	1427	3955	lpfC	0/0	100.0	98.5	NP_462539	(lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_221410 cov_19.5443	5043	5570	lpfE	0/0	100.0	99.2	NP_462537	(lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_107697 cov_21.0948	62295	65021	mgtB	0/0	100.0	98.8	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_107697 cov_21.0948	65241	65936	mgtC	0/0	100.0	99.0	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_30 length_59122 cov_17.1178	17240	18136	mig-14	0/0	100.0	97.7	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_107697 cov_21.0948	55515	58382	misL	3/30	99.5	97.4	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	1221	1820	orgA	0/0	100.0	99.5	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	574	1264	orgB	1/10	100.0	97.5	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	125	577	orgC	0/0	100.0	98.0	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_38 length_40142 cov_14.9506	27	902	pipB	0/0	100.0	98.7	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_30 length_59122 cov_17.1178	19877	20929	pipB2	0/0	100.0	93.9	NP_461706	(pipB2) type III secretion system effector PipB3 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	3138	4316	prgH	0/0	100.0	99.3	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	2871	3113	prgI	0/0	100.0	98.8	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	2547	2852	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	1792	2550	prgK	0/0	100.0	99.5	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	17693	18190	sicA	0/0	100.0	99.4	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	10484	10876	sicP	0/0	100.0	99.5	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_97993 cov_15.5134	79280	80290	sifA	0/0	100.0	96.1	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_27 length_65470 cov_13.5488	37250	38200	sifB	0/0	100.0	95.7	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_31 length_56892 cov_19.3255	54570	56762	sinH	0/0	100.0	97.6	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	11474	13531	sipA/sspA	0/0	100.0	99.2	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	15909	17690	sipB/sspB	0/0	100.0	99.5	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	14652	15881	sipC/sspC	0/0	100.0	99.7	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	13550	14581	sipD	0/0	100.0	98.7	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_29 length_59659 cov_15.7924	22818	25085	slrP	1/30	98.7	95.3	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_93408 cov_15.3063	72591	74939	sopA	0/0	100.0	98.1	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_77 length_11117 cov_13.6384	1269	2954	sopB/sigD	0/0	100.0	97.6	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_149413 cov_18.3288	109838	110791	sopD	0/0	100.0	98.2	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_37 length_42934 cov_15.5373	36233	37192	sopD2	0/0	100.0	92.6	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_24 length_70283 cov_13.578	340	1062	sopE2	0/0	100.0	96.7	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	21130	22041	spaO	0/0	100.0	99.5	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	20466	21140	spaP	0/0	100.0	99.4	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	20180	20440	spaQ	0/0	100.0	99.2	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	19385	20176	spaR	0/0	100.0	99.6	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	18328	19398	spaS	0/0	100.0	99.9	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	20079	20480	spiC/ssaB	0/0	100.0	99.8	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_47 length_31672 cov_17.482	8866	10497	sptP	0/0	100.0	98.4	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	20482	21975	ssaC	0/0	100.0	98.7	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	21956	23167	ssaD	0/0	100.0	98.7	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	23175	23417	ssaE	0/0	100.0	98.8	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	1454	1669	ssaG	0/0	100.0	99.1	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	1710	1937	ssaH	0/0	100.0	99.1	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	1949	2197	ssaI	0/0	100.0	98.4	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	2194	2943	ssaJ	0/0	100.0	98.5	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	3506	4180	ssaK	0/0	100.0	98.8	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	4146	5162	ssaL	0/0	100.0	99.0	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	5220	5588	ssaM	0/0	100.0	98.6	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	7608	8909	ssaN	0/0	100.0	98.5	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	8912	9289	ssaO	0/0	100.0	99.2	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	9270	9644	ssaP	0/0	100.0	98.7	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	9625	10593	ssaQ	0/0	100.0	98.6	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	10661	11308	ssaR	0/0	100.0	99.5	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	11305	11571	ssaS	0/0	100.0	100.0	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	11572	12351	ssaT	0/0	100.0	98.1	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	12348	13406	ssaU	0/0	100.0	97.7	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	5573	7618	ssaV	0/0	100.0	99.1	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	24600	25073	sscA	0/0	100.0	97.7	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	27604	28038	sscB	0/0	100.0	99.8	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	23680	24006	sseA	0/0	100.0	98.8	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	24013	24603	sseB	0/0	100.0	96.6	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	25076	26530	sseC	0/0	100.0	95.7	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	26546	27133	sseD	0/0	100.0	95.4	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_28146 cov_13.2336	27136	27552	sseE	0/0	100.0	98.3	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_146295 cov_14.287	672	1361	sseG	0/0	100.0	97.7	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_59 length_25477 cov_12.8437	23348	24574	sseJ	0/0	100.0	96.4	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_32563 cov_20.8608	13692	14702	sseK1	0/0	100.0	99.2	NP_463026	(sseK1) type III secretion system effector SseK1 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_81721 cov_15.305	77105	78151	sseK2	0/0	100.0	99.1	NP_461081	(sseK2) type III secretion system effector SseK2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_27 length_65470 cov_13.5488	14577	15209	steA	0/0	100.0	97.5	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_27 length_65470 cov_13.5488	64690	65091	steB	0/0	100.0	97.0	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

MS0499

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_24 length_65303 cov_20.364	2259	3167	avrA	0/0	100.0	99.5	NP_461786	(avrA) type III secretion system effector AvrA acetyltransferease [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_161343 cov_21.58	121399	121941	bcfA	0/0	100.0	99.5	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_161343 cov_21.58	122042	122728	bcfB	0/0	100.0	99.6	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_161343 cov_21.58	122733	125354	bcfC	0/0	100.0	98.9	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_161343 cov_21.58	125355	126362	bcfD	0/0	100.0	98.6	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_161343 cov_21.58	126363	126908	bcfE	0/0	100.0	98.2	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_161343 cov_21.58	126924	127442	bcfF	0/0	100.0	98.1	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_161343 cov_21.58	127408	128139	bcfG	0/0	100.0	98.4	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	179320	179775	csgA	0/0	100.0	98.7	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	179817	180272	csgB	0/0	100.0	100.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	178932	179258	csgC	0/0	100.0	100.0	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	181027	181677	csgD	0/0	100.0	99.2	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	181682	182077	csgE	0/0	100.0	100.0	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	182104	182520	csgF	0/0	100.0	99.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	182547	183380	csgG	0/0	100.0	99.6	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403701 cov_18.9992	134024	134716	fimC	0/0	100.0	98.7	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403701 cov_18.9992	131381	133993	fimD	0/0	100.0	98.9	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403701 cov_18.9992	129831	130349	fimF	0/0	100.0	98.3	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403701 cov_18.9992	130359	131366	fimH	0/0	100.0	97.9	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403701 cov_18.9992	134760	135293	fimI	0/0	100.0	99.1	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	61853	63910	invA	0/0	100.0	99.6	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	63934	64341	invB	0/0	100.0	99.3	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	64338	65633	invC	0/0	100.0	99.4	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	60710	61828	invE	0/0	100.0	99.7	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	58378	59028	invF	0/0	100.0	99.7	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	59025	60713	invG	0/0	100.0	99.5	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	57477	57920	invH	0/0	100.0	99.3	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	65611	66054	invI	0/0	100.0	99.3	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	66054	67064	invJ	0/0	100.0	99.3	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_414408 cov_22.6359	192952	193488	lpfA	0/0	100.0	96.8	NP_462541	(lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_414408 cov_22.6359	193572	194270	lpfB	0/0	100.0	98.7	NP_462540	(lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_414408 cov_22.6359	194293	196821	lpfC	0/0	100.0	98.5	NP_462539	(lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_414408 cov_22.6359	197909	198436	lpfE	0/0	100.0	99.2	NP_462537	(lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_414408 cov_22.6359	42586	45312	mgtB	0/0	100.0	98.8	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_414408 cov_22.6359	41671	42366	mgtC	0/0	100.0	99.0	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_38 length_34757 cov_18.7664	17496	18392	mig-14	0/0	100.0	97.7	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_414408 cov_22.6359	49225	52092	misL	3/30	99.5	97.4	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	87285	87884	orgA	0/0	100.0	99.5	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	87841	88531	orgB	1/10	100.0	97.5	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	88528	88980	orgC	0/0	100.0	98.0	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_18 length_79532 cov_16.1545	39197	40072	pipB	0/0	100.0	98.7	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_38 length_34757 cov_18.7664	20133	21185	pipB2	0/0	100.0	93.9	NP_461706	(pipB2) type III secretion system effector PipB3 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	84789	85967	prgH	0/0	100.0	99.3	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	85992	86234	prgI	0/0	100.0	98.8	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	86253	86558	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	86555	87313	prgK	0/0	100.0	99.5	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	70915	71412	sicA	0/0	100.0	99.4	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	78229	78621	sicP	0/0	100.0	99.5	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_236778 cov_16.7821	100548	101558	sifA	0/0	100.0	96.1	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_224057 cov_15.0684	102521	103471	sifB	0/0	100.0	95.7	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_266182 cov_18.7292	263900	266092	sinH	0/0	100.0	97.6	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	75574	77631	sipA/sspA	0/0	100.0	99.2	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	71415	73196	sipB/sspB	0/0	100.0	99.5	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	73224	74453	sipC/sspC	0/0	100.0	99.7	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	74524	75555	sipD	0/0	100.0	98.7	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_28 length_59659 cov_16.8412	22818	25085	slrP	1/30	98.7	95.3	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_32 length_50055 cov_17.0223	22753	25101	sopA	0/0	100.0	98.1	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_18 length_79532 cov_16.1545	41411	43096	sopB/sigD	0/0	100.0	97.6	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	13307	14260	sopD	0/0	100.0	98.2	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_34 length_42991 cov_17.1474	36290	37249	sopD2	0/0	100.0	92.6	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_162718 cov_15.3676	68344	69066	sopE2	0/0	100.0	96.7	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	67064	67975	spaO	0/0	100.0	99.5	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	67965	68639	spaP	0/0	100.0	99.4	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	68665	68925	spaQ	0/0	100.0	99.2	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	68929	69720	spaR	0/0	100.0	99.6	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	69707	70777	spaS	0/0	100.0	99.9	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	7627	8028	spiC/ssaB	0/0	100.0	99.8	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_89140 cov_19.6667	78608	80239	sptP	0/0	100.0	98.4	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	6132	7625	ssaC	0/0	100.0	98.7	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	4940	6151	ssaD	0/0	100.0	98.7	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	4690	4932	ssaE	0/0	100.0	98.8	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	61247	61462	ssaG	0/0	100.0	99.1	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	60979	61206	ssaH	0/0	100.0	99.1	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	60719	60967	ssaI	0/0	100.0	98.4	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	59973	60722	ssaJ	0/0	100.0	98.5	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	58736	59410	ssaK	0/0	100.0	98.8	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	57754	58770	ssaL	0/0	100.0	99.0	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	57328	57696	ssaM	0/0	100.0	98.6	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	54007	55308	ssaN	0/0	100.0	98.5	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	53627	54004	ssaO	0/0	100.0	99.2	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	53272	53646	ssaP	0/0	100.0	98.7	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	52323	53291	ssaQ	0/0	100.0	98.6	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	51608	52255	ssaR	0/0	100.0	99.5	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	51345	51611	ssaS	0/0	100.0	100.0	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	50565	51344	ssaT	0/0	100.0	98.1	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	49510	50568	ssaU	0/0	100.0	97.7	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	55298	57343	ssaV	0/0	100.0	99.1	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	3034	3507	sscA	0/0	100.0	97.7	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	69	503	sscB	0/0	100.0	99.8	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	4101	4427	sseA	0/0	100.0	98.8	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	3504	4094	sseB	0/0	100.0	96.6	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	1577	3031	sseC	0/0	100.0	95.7	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	974	1561	sseD	0/0	100.0	95.4	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_77226 cov_15.7157	555	971	sseE	0/0	100.0	98.3	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_62916 cov_16.1028	61555	62244	sseG	0/0	100.0	97.7	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_224057 cov_15.0684	73133	74359	sseJ	0/0	100.0	96.4	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_54 length_19022 cov_21.3638	151	1161	sseK1	0/0	100.0	99.2	NP_463026	(sseK1) type III secretion system effector SseK1 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_112967 cov_16.7429	108026	109072	sseK2	0/0	100.0	99.1	NP_461081	(sseK2) type III secretion system effector SseK2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_224057 cov_15.0684	125512	126144	steA	0/0	100.0	97.5	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_224057 cov_15.0684	75630	76031	steB	0/0	100.0	97.0	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_224057 cov_15.0684	43	1416	steC	0/0	100.0	95.8	NP_460656	(steC) type III secretion system effector SteC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

MS0500

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_15 length_144214 cov_21.7517	140848	141756	avrA	0/0	100.0	99.7	NP_461786	(avrA) type III secretion system effector AvrA acetyltransferease [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_174151 cov_23.2331	134896	135438	bcfA	0/0	100.0	99.6	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_174151 cov_23.2331	135539	136225	bcfB	0/0	100.0	99.7	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_174151 cov_23.2331	136230	138851	bcfC	0/0	100.0	99.2	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_174151 cov_23.2331	138852	139859	bcfD	0/0	100.0	99.2	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_174151 cov_23.2331	139860	140405	bcfE	0/0	100.0	98.3	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_174151 cov_23.2331	140421	140939	bcfF	0/0	100.0	99.8	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_174151 cov_23.2331	140905	141636	bcfG	0/0	100.0	99.3	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_189929 cov_19.4046	188521	188976	csgA	0/0	100.0	98.9	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_189929 cov_19.4046	189018	189473	csgB	0/0	100.0	99.6	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_189929 cov_19.4046	188133	188459	csgC	0/0	100.0	100.0	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_55592 cov_21.612	300	950	csgD	0/0	100.0	99.7	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_55592 cov_21.612	955	1350	csgE	0/0	100.0	100.0	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_55592 cov_21.612	1377	1793	csgF	0/0	100.0	100.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_55592 cov_21.612	1820	2653	csgG	0/0	100.0	99.6	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_439190 cov_21.4436	285612	286304	fimC	0/0	100.0	99.0	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_439190 cov_21.4436	286335	288947	fimD	0/0	100.0	99.0	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_439190 cov_21.4436	289979	290497	fimF	0/0	100.0	99.2	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_439190 cov_21.4436	288962	289969	fimH	0/0	100.0	98.2	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_439190 cov_21.4436	285035	285568	fimI	0/0	100.0	98.3	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	6562	8619	invA	0/0	100.0	99.4	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	8643	9050	invB	0/0	100.0	99.0	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	9047	10342	invC	0/0	100.0	99.8	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	5419	6537	invE	0/0	100.0	99.7	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	3087	3737	invF	0/0	100.0	100.0	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	3734	5422	invG	0/0	100.0	99.3	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	2188	2631	invH	0/0	100.0	98.7	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	10320	10763	invI	0/0	100.0	100.0	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	10763	11773	invJ	0/0	100.0	99.2	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_228058 cov_24.3475	102	638	lpfA	0/0	100.0	99.8	NP_462541	(lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_228058 cov_24.3475	723	1421	lpfB	0/0	100.0	99.9	NP_462540	(lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_228058 cov_24.3475	1444	3972	lpfC	0/0	100.0	99.2	NP_462539	(lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_228058 cov_24.3475	3990	5069	lpfD	0/0	100.0	99.6	NP_462538	(lpfD) long polar fimbrial protein LpfD [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_5 length_228058 cov_24.3475	5075	5602	lpfE	0/0	100.0	99.8	NP_462537	(lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_178040 cov_24.3631	132630	135356	mgtB	0/0	100.0	99.0	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_178040 cov_24.3631	135576	136271	mgtC	0/0	100.0	98.6	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_144214 cov_21.7517	60674	61570	mig-14	0/0	100.0	98.1	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_178040 cov_24.3631	125910	128777	misL	0/0	100.0	99.4	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	31996	32595	orgA	0/0	100.0	99.8	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	32552	33232	orgB	0/0	100.0	99.8	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	33229	33681	orgC	0/0	100.0	99.3	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_89962 cov_18.85	33424	34299	pipB	0/0	100.0	98.6	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_144214 cov_21.7517	57880	58932	pipB2	0/0	100.0	99.5	NP_461706	(pipB2) type III secretion system effector PipB3 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	29500	30678	prgH	0/0	100.0	99.6	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	30703	30945	prgI	0/0	100.0	100.0	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	30964	31269	prgJ	0/0	100.0	99.0	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	31266	32024	prgK	0/0	100.0	99.6	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_245609 cov_20.9797	106332	113639	ratB	0/0	100.0	99.0	NP_461449	(ratB) putative outer membrane protein [RatB (VF0399)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	15624	16121	sicA	0/0	100.0	99.6	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	22938	23330	sicP	0/0	100.0	99.8	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_8 length_189929 cov_19.4046	109766	110776	sifA	0/0	100.0	99.8	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	65745	66695	sifB	0/0	100.0	97.7	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	20283	22340	sipA/sspA	0/0	100.0	99.8	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	16124	17905	sipB/sspB	0/0	100.0	99.7	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	17933	19162	sipC/sspC	0/0	100.0	99.5	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	19233	20264	sipD	0/0	100.0	99.8	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_23 length_65031 cov_19.5225	33913	36167	slrP	3/43	98.1	96.3	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_170699 cov_18.423	45563	46096	sodCI	0/0	100.0	100.0	NP_460019	(sodCI) Gifsy-2 prophage: superoxide dismutase precursor (Cu-Zn) [SodCI (VF0109)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_197194 cov_20.3343	194356	196704	sopA	0/0	100.0	99.2	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_89962 cov_18.85	35205	36890	sopB/sigD	0/0	100.0	99.6	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_18 length_109850 cov_22.9478	108826	109779	sopD	0/0	100.0	98.1	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_163604 cov_19.6098	111954	112913	sopD2	0/0	100.0	99.4	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_170699 cov_18.423	20092	20814	sopE2	0/0	100.0	99.9	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	11773	12684	spaO	0/0	100.0	98.9	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	12674	13348	spaP	0/0	100.0	99.0	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	13374	13634	spaQ	0/0	100.0	100.0	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	13638	14429	spaR	0/0	100.0	99.4	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	14416	15486	spaS	0/0	100.0	99.9	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	273831	274232	spiC/ssaB	0/0	100.0	99.5	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_33 length_33794 cov_21.3072	23317	24948	sptP	0/0	100.0	99.6	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	272336	273829	ssaC	0/0	100.0	98.9	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	271144	272355	ssaD	0/0	100.0	99.5	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	270894	271136	ssaE	0/0	100.0	100.0	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	264540	264755	ssaG	0/0	100.0	99.5	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	264272	264499	ssaH	0/0	100.0	100.0	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	264012	264260	ssaI	0/0	100.0	100.0	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	263266	264015	ssaJ	0/0	100.0	98.8	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	262029	262703	ssaK	0/0	100.0	99.6	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	261047	262063	ssaL	0/0	100.0	99.4	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	260621	260989	ssaM	0/0	100.0	99.7	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	257300	258601	ssaN	0/0	100.0	98.6	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	256920	257297	ssaO	0/0	100.0	99.7	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	256565	256939	ssaP	0/0	100.0	99.5	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	255616	256584	ssaQ	0/0	100.0	98.0	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	254901	255548	ssaR	0/0	100.0	98.9	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	254638	254904	ssaS	0/0	100.0	99.6	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	253858	254637	ssaT	0/0	100.0	98.8	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	252803	253861	ssaU	0/0	100.0	99.2	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	258591	260636	ssaV	0/0	100.0	99.8	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	269298	269771	sscA	0/0	100.0	99.2	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	266333	266767	sscB	0/0	100.0	100.0	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	270365	270691	sseA	0/0	100.0	99.7	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	269768	270358	sseB	0/0	100.0	100.0	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	267841	269295	sseC	0/0	100.0	99.1	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	267238	267825	sseD	0/0	100.0	100.0	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	266819	267235	sseE	0/0	100.0	99.8	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	265535	266317	sseF	0/0	100.0	99.2	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	264849	265538	sseG	0/0	100.0	99.4	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_163604 cov_19.6098	160554	161522	sseI/srfH	0/0	100.0	99.7	NP_460026	(sseI/srfH) type III secretion system effector SseI/SrfH cysteine protease [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	31625	32851	sseJ	0/0	100.0	99.7	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_155456 cov_20.67	41305	42258	sseL	0/0	100.0	96.5	NP_461229	(sseL) type III secretion system effector SseL deubiquitinase [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_197194 cov_20.3343	4336	6702	sspH2	0/0	100.0	99.7	NP_461184	(sspH2) type III secretion system effector SspH2 E3 ubiquitin ligase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	88719	89351	steA	0/0	100.0	97.5	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_343106 cov_18.4156	34122	34522	steB	1/1	99.8	99.8	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_191046 cov_18.0569	48393	49766	steC	0/0	100.0	99.4	NP_460656	(steC) type III secretion system effector SteC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

MS0501

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_65 length_22305 cov_19.0694	6804	7346	bcfA	0/0	100.0	98.9	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_65 length_22305 cov_19.0694	7447	8133	bcfB	0/0	100.0	99.8	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_65 length_22305 cov_19.0694	8138	10759	bcfC	0/0	100.0	98.3	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_65 length_22305 cov_19.0694	10760	11767	bcfD	0/0	100.0	97.9	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_65 length_22305 cov_19.0694	11768	12313	bcfE	0/0	100.0	98.5	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_65 length_22305 cov_19.0694	12329	12847	bcfF	0/0	100.0	98.3	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_65 length_22305 cov_19.0694	12813	13544	bcfG	0/0	100.0	98.5	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_109 length_3491 cov_10.6106	180	989	cdtB	0/0	100.0	100.0	NP_456275	(cdtB) cytolethal distending toxin B [CdtB (VF0407)] [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
NODE_6 length_135378 cov_17.0184	101888	102343	csgA	0/0	100.0	98.9	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_135378 cov_17.0184	102385	102840	csgB	0/0	100.0	99.3	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_135378 cov_17.0184	101500	101826	csgC	0/0	100.0	99.4	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_135378 cov_17.0184	103595	104245	csgD	0/0	100.0	99.1	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_135378 cov_17.0184	104250	104645	csgE	0/0	100.0	99.5	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_135378 cov_17.0184	104672	105088	csgF	0/0	100.0	100.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_135378 cov_17.0184	105115	105948	csgG	0/0	100.0	99.6	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_194862 cov_19.9979	15129	15821	fimC	0/0	100.0	98.4	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_194862 cov_19.9979	12486	15098	fimD	0/0	100.0	98.7	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_194862 cov_19.9979	10937	11454	fimF	0/0	99.8	98.5	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_194862 cov_19.9979	11464	12471	fimH	0/0	100.0	98.2	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_194862 cov_19.9979	15865	16398	fimI	0/0	100.0	99.1	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	8044	10101	invA	0/0	100.0	99.4	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	10125	10532	invB	0/0	100.0	99.3	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	10529	11824	invC	0/0	100.0	99.2	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	6901	8019	invE	0/0	100.0	99.3	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	4569	5219	invF	0/0	100.0	99.5	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	5216	6904	invG	0/0	100.0	98.9	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	3669	4112	invH	0/0	100.0	98.7	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	11802	12245	invI	0/0	100.0	99.5	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	12245	13255	invJ	0/0	100.0	98.7	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_54162 cov_23.2666	1860	4586	mgtB	0/0	100.0	98.7	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_26 length_54162 cov_23.2666	4807	5502	mgtC	0/0	100.0	98.6	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_98963 cov_19.7083	81703	82599	mig-14	0/0	100.0	97.2	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_98 length_6029 cov_19.8197	1179	4031	misL	1/15	99.5	97.6	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	33467	34066	orgA	0/0	100.0	99.5	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	34023	34713	orgB	1/10	100.0	98.0	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	34710	35162	orgC	0/0	100.0	98.7	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_43 length_36329 cov_17.0979	241	1116	pipB	0/0	100.0	98.5	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	30971	32149	prgH	0/0	100.0	99.2	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	32174	32416	prgI	0/0	100.0	100.0	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	32435	32740	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	32737	33495	prgK	0/0	100.0	99.6	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	17106	17603	sicA	0/0	100.0	99.4	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	24411	24803	sicP	0/0	100.0	99.2	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_135378 cov_17.0184	16778	17788	sifA	0/0	100.0	96.7	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_50 length_31448 cov_14.8458	270	1220	sifB	0/0	100.0	95.7	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_78 length_14674 cov_20.275	131	2323	sinH	0/0	100.0	95.6	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	21756	23813	sipA/sspA	0/0	100.0	98.3	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	17606	19387	sipB/sspB	0/0	100.0	99.4	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	19415	20644	sipC/sspC	0/0	100.0	99.5	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	20715	21737	sipD	3/11	99.0	90.3	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_93603 cov_16.4803	32533	34800	slrP	2/30	98.7	94.6	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_21 length_65339 cov_17.9413	45745	48093	sopA	0/0	100.0	97.2	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_87 length_10509 cov_16.2412	8158	9843	sopB/sigD	0/0	100.0	98.2	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_28 length_53692 cov_20.9044	12105	13058	sopD	0/0	100.0	97.7	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_46 length_34888 cov_15.0279	13902	14624	sopE2	0/0	100.0	98.1	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	13255	14166	spaO	0/0	100.0	98.7	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	14156	14830	spaP	0/0	100.0	98.7	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	14856	15116	spaQ	0/0	100.0	99.6	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	15120	15911	spaR	0/0	100.0	99.0	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	15898	16968	spaS	0/0	100.0	98.5	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	20079	20480	spiC/ssaB	0/0	100.0	99.2	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_45 length_35322 cov_18.0817	24790	26421	sptP	0/0	100.0	97.6	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	18584	20077	ssaC	0/0	100.0	98.5	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	17392	18603	ssaD	0/0	100.0	98.2	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	17142	17384	ssaE	0/0	100.0	99.2	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	10788	11003	ssaG	0/0	100.0	100.0	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	10520	10747	ssaH	0/0	100.0	99.6	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	10260	10508	ssaI	0/0	100.0	98.8	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	9514	10263	ssaJ	0/0	100.0	98.1	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	8277	8951	ssaK	0/0	100.0	98.5	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	7295	8311	ssaL	0/0	100.0	99.0	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	6869	7237	ssaM	0/0	100.0	97.0	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	3548	4849	ssaN	0/0	100.0	98.8	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	3168	3545	ssaO	0/0	100.0	98.2	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	2813	3187	ssaP	0/0	100.0	99.5	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	1864	2832	ssaQ	0/0	100.0	98.1	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	1149	1796	ssaR	0/0	100.0	98.9	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	886	1152	ssaS	0/0	100.0	99.2	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	106	885	ssaT	0/0	100.0	97.6	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	4839	6884	ssaV	0/0	100.0	99.0	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	15546	16019	sscA	0/0	100.0	97.5	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	12581	13015	sscB	0/0	100.0	99.5	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	16613	16939	sseA	0/0	100.0	99.7	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	16016	16606	sseB	0/0	100.0	97.1	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	14089	15543	sseC	0/0	100.0	97.2	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	13486	14073	sseD	0/0	100.0	96.9	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	13067	13483	sseE	0/0	100.0	99.3	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	11783	12565	sseF	0/0	100.0	98.5	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_68 length_20602 cov_15.0866	11097	11786	sseG	0/0	100.0	96.7	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_50 length_31448 cov_14.8458	29381	30607	sseJ	0/0	100.0	96.8	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_39 length_36904 cov_16.6877	14585	15217	steA	0/0	100.0	94.5	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_50 length_31448 cov_14.8458	27709	28110	steB	0/0	100.0	97.5	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_95 length_7171 cov_12.9265	51	1424	steC	0/0	100.0	95.0	NP_460656	(steC) type III secretion system effector SteC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

MS0502

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_15 length_153308 cov_19.2231	2391	3299	avrA	0/0	100.0	99.6	NP_461786	(avrA) type III secretion system effector AvrA acetyltransferease [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_204883 cov_21.5508	34762	35304	bcfA	0/0	100.0	99.1	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_204883 cov_21.5508	33975	34661	bcfB	0/0	100.0	99.7	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_204883 cov_21.5508	31349	33970	bcfC	0/0	100.0	99.2	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_204883 cov_21.5508	30341	31348	bcfD	0/0	100.0	98.5	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_204883 cov_21.5508	29795	30340	bcfE	0/0	100.0	98.5	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_204883 cov_21.5508	29261	29779	bcfF	0/0	100.0	99.8	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_7 length_204883 cov_21.5508	28564	29295	bcfG	0/0	100.0	99.0	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	1041	1496	csgA	0/0	100.0	99.1	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	544	999	csgB	0/0	100.0	99.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	1558	1884	csgC	0/0	100.0	99.7	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_158383 cov_15.6154	192	842	csgD	0/0	100.0	99.7	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_158383 cov_15.6154	847	1242	csgE	0/0	100.0	100.0	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_158383 cov_15.6154	1269	1685	csgF	0/0	100.0	99.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_158383 cov_15.6154	1712	2545	csgG	0/0	100.0	99.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_311708 cov_19.7568	114309	115001	fimC	0/0	100.0	98.4	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_311708 cov_19.7568	115032	117644	fimD	0/0	100.0	98.8	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_311708 cov_19.7568	118676	119194	fimF	0/0	100.0	99.4	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_311708 cov_19.7568	117659	118666	fimH	0/0	100.0	98.2	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_311708 cov_19.7568	113732	114265	fimI	0/0	100.0	98.5	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	25193	27250	invA	0/0	100.0	99.2	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	24762	25169	invB	0/0	100.0	99.0	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	23470	24765	invC	0/0	100.0	99.2	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	27275	28393	invE	0/0	100.0	99.4	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	30075	30725	invF	0/0	100.0	98.9	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	28390	30078	invG	0/0	100.0	99.3	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	31183	31626	invH	0/0	100.0	98.9	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	23049	23492	invI	0/0	100.0	99.5	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	22039	23049	invJ	0/0	100.0	99.2	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_17 length_101920 cov_24.0111	48470	51196	mgtB	0/0	100.0	99.4	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_17 length_101920 cov_24.0111	47555	48250	mgtC	0/0	100.0	99.0	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_153308 cov_19.2231	82570	83466	mig-14	0/0	100.0	97.8	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_17 length_101920 cov_24.0111	55110	57977	misL	0/0	100.0	99.2	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	1219	1818	orgA	0/0	100.0	100.0	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	582	1262	orgB	0/0	100.0	99.7	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	133	585	orgC	0/0	100.0	99.3	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_158383 cov_15.6154	52697	53572	pipB	0/0	100.0	98.6	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_15 length_153308 cov_19.2231	85208	86260	pipB2	0/0	100.0	98.3	NP_461706	(pipB2) type III secretion system effector PipB3 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	3136	4314	prgH	0/0	100.0	99.6	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	2869	3111	prgI	0/0	100.0	100.0	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	2545	2850	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	1790	2548	prgK	0/0	100.0	99.9	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_360607 cov_17.3835	107423	113551	shdA	5/13	100.0	94.2	NP_461448	(shdA) AIDA autotransporter-like protein [ShdA (VF0398)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	17691	18188	sicA	0/0	100.0	99.2	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	10482	10874	sicP	0/0	100.0	100.0	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	79252	80262	sifA	0/0	100.0	99.8	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	459081	460031	sifB	0/0	100.0	97.2	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_360607 cov_17.3835	97419	99611	sinH	0/0	100.0	98.3	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	11472	13529	sipA/sspA	0/0	100.0	99.8	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	15907	17688	sipB/sspB	0/0	100.0	99.2	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	14650	15879	sipC/sspC	0/0	100.0	99.6	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	13548	14579	sipD	0/0	100.0	99.8	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_179196 cov_15.8455	57314	59581	slrP	2/30	98.7	96.9	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_395533 cov_15.2345	19754	22102	sopA	0/0	100.0	99.3	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_158383 cov_15.6154	50106	51791	sopB/sigD	0/0	100.0	99.8	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	73106	74059	sopD	0/0	100.0	98.6	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_158383 cov_15.6154	129223	130182	sopD2	0/0	100.0	99.7	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_395533 cov_15.2345	232459	233181	sopE2	0/0	100.0	99.7	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	21128	22039	spaO	0/0	100.0	99.0	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	20464	21138	spaP	0/0	100.0	99.1	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	20178	20438	spaQ	0/0	100.0	100.0	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	19383	20174	spaR	0/0	100.0	99.8	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	18326	19396	spaS	0/0	100.0	100.0	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	247342	247741	spiC/ssaB	0/0	99.5	99.8	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_195208 cov_20.4639	8864	10495	sptP	0/0	100.0	99.8	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	247743	249236	ssaC	0/0	100.0	99.0	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	249217	250428	ssaD	0/0	100.0	99.2	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	250436	250678	ssaE	0/0	100.0	100.0	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	256877	257092	ssaG	0/0	100.0	100.0	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	257133	257360	ssaH	0/0	100.0	99.6	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	257372	257620	ssaI	0/0	100.0	100.0	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	257617	258366	ssaJ	0/0	100.0	99.3	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	258929	259603	ssaK	0/0	100.0	99.6	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	259569	260585	ssaL	0/0	100.0	99.1	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	260643	261011	ssaM	0/0	100.0	99.7	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	263031	264332	ssaN	0/0	100.0	99.5	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	264335	264712	ssaO	0/0	100.0	100.0	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	264693	265067	ssaP	0/0	100.0	99.7	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	265048	266016	ssaQ	0/0	100.0	98.5	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	266084	266731	ssaR	0/0	100.0	98.9	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	266728	266994	ssaS	0/0	100.0	99.6	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	266995	267774	ssaT	0/0	100.0	98.7	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	267771	268829	ssaU	0/0	100.0	99.2	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	260996	263041	ssaV	0/0	100.0	99.5	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	251861	252334	sscA	0/0	100.0	98.9	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	254865	255299	sscB	0/0	100.0	100.0	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	250941	251267	sseA	0/0	100.0	99.7	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	251274	251864	sseB	0/0	100.0	100.0	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	252337	253791	sseC	0/0	100.0	98.1	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	253807	254394	sseD	0/0	100.0	97.5	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	254397	254813	sseE	0/0	100.0	98.8	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	255315	256097	sseF	0/0	100.0	99.4	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	256094	256783	sseG	0/0	100.0	99.3	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	488194	489420	sseJ	0/0	100.0	99.4	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_163065 cov_16.7552	56384	57430	sseK2	0/0	100.0	100.0	NP_461081	(sseK2) type III secretion system effector SseK2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_360607 cov_17.3835	344329	345282	sseL	0/0	100.0	97.6	NP_461229	(sseL) type III secretion system effector SseL deubiquitinase [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_163065 cov_16.7552	156156	158522	sspH2	0/0	100.0	99.7	NP_461184	(sspH2) type III secretion system effector SspH2 E3 ubiquitin ligase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	436424	437043	steA	2/15	97.8	96.2	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_558286 cov_14.6997	486522	486923	steB	0/0	100.0	99.8	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_31 length_12556 cov_10.5521	5349	6270	tcpC	2/2	99.8	95.9	NP_754290	(tcpC) Tir domain containing protein TcpC [TcpC (VF0413)] [Escherichia coli CFT073]

MS0503

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_6 length_226104 cov_17.4582	75187	76095	avrA	0/0	100.0	99.6	NP_461786	(avrA) type III secretion system effector AvrA acetyltransferease [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_180289 cov_18.9663	34762	35304	bcfA	0/0	100.0	99.1	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_180289 cov_18.9663	33975	34661	bcfB	0/0	100.0	99.7	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_180289 cov_18.9663	31349	33970	bcfC	0/0	100.0	99.2	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_180289 cov_18.9663	30341	31348	bcfD	0/0	100.0	98.5	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_180289 cov_18.9663	29795	30340	bcfE	0/0	100.0	98.5	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_180289 cov_18.9663	29261	29779	bcfF	0/0	100.0	99.8	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_180289 cov_18.9663	28564	29295	bcfG	0/0	100.0	99.0	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	162244	162699	csgA	0/0	100.0	99.1	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	161747	162202	csgB	0/0	100.0	99.8	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	162761	163087	csgC	0/0	100.0	99.7	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	160342	160992	csgD	0/0	100.0	99.7	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	159942	160337	csgE	0/0	100.0	100.0	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	159499	159915	csgF	0/0	100.0	99.8	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	158639	159472	csgG	0/0	100.0	99.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_326616 cov_17.8675	211599	212291	fimC	0/0	100.0	98.4	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_326616 cov_17.8675	208956	211568	fimD	0/0	100.0	98.8	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_326616 cov_17.8675	207406	207924	fimF	0/0	100.0	99.4	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_326616 cov_17.8675	207934	208941	fimH	0/0	100.0	98.2	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_326616 cov_17.8675	212335	212868	fimI	0/0	100.0	98.5	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	45537	47594	invA	0/0	100.0	99.2	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	47618	48025	invB	0/0	100.0	99.0	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	48022	49317	invC	0/0	100.0	99.2	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	44394	45512	invE	0/0	100.0	99.4	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	42062	42712	invF	0/0	100.0	98.9	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	42709	44397	invG	0/0	100.0	99.3	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	41161	41604	invH	0/0	100.0	98.9	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	49295	49738	invI	0/0	100.0	99.5	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	49738	50748	invJ	0/0	100.0	99.2	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_18 length_101167 cov_21.2632	48251	50977	mgtB	0/0	100.0	99.4	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_18 length_101167 cov_21.2632	47336	48031	mgtC	0/0	100.0	99.0	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	155366	156262	mig-14	0/0	100.0	97.8	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_18 length_101167 cov_21.2632	54891	57758	misL	0/0	100.0	99.2	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	70969	71568	orgA	0/0	100.0	100.0	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	71525	72205	orgB	0/0	100.0	99.7	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	72202	72654	orgC	0/0	100.0	99.3	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	107612	108487	pipB	0/0	100.0	98.6	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	158004	159056	pipB2	0/0	100.0	98.3	NP_461706	(pipB2) type III secretion system effector PipB3 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	68473	69651	prgH	0/0	100.0	99.6	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	69676	69918	prgI	0/0	100.0	100.0	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	69937	70242	prgJ	0/0	100.0	99.7	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	70239	70997	prgK	0/0	100.0	99.9	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_301022 cov_16.4564	187472	193600	shdA	5/13	100.0	94.2	NP_461448	(shdA) AIDA autotransporter-like protein [ShdA (VF0398)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	54599	55096	sicA	0/0	100.0	99.2	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	61913	62305	sicP	0/0	100.0	100.0	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	240455	241465	sifA	0/0	100.0	99.8	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	190025	190975	sifB	0/0	100.0	97.2	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_4 length_301022 cov_16.4564	201412	203604	sinH	0/0	100.0	98.3	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	59258	61315	sipA/sspA	0/0	100.0	99.8	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	55099	56880	sipB/sspB	0/0	100.0	99.2	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	56908	58137	sipC/sspC	0/0	100.0	99.6	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	58208	59239	sipD	0/0	100.0	99.8	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_197559 cov_14.6957	75709	77976	slrP	2/30	98.7	96.9	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_24 length_46382 cov_14.9347	17962	20310	sopA	0/0	100.0	99.3	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	109393	111078	sopB/sigD	0/0	100.0	99.8	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_17 length_122553 cov_18.3323	329	1282	sopD	0/0	100.0	98.6	NP_461866	(sopD) type III secretion system effector SopD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_408239 cov_14.1248	31002	31961	sopD2	0/0	100.0	99.7	NP_459947	(sopD2) type III secretion system effector SopD2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_10 length_196382 cov_14.5915	126303	127025	sopE2	0/0	100.0	99.7	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	50748	51659	spaO	0/0	100.0	99.0	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	51649	52323	spaP	0/0	100.0	99.1	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	52349	52609	spaQ	0/0	100.0	100.0	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	52613	53404	spaR	0/0	100.0	99.8	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	53391	54461	spaS	0/0	100.0	100.0	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	402408	402807	spiC/ssaB	0/0	99.5	99.8	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_6 length_226104 cov_17.4582	62292	63923	sptP	0/0	100.0	99.8	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	400913	402406	ssaC	0/0	100.0	99.0	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	399721	400932	ssaD	0/0	100.0	99.2	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	399471	399713	ssaE	0/0	100.0	100.0	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	393057	393272	ssaG	0/0	100.0	100.0	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	392789	393016	ssaH	0/0	100.0	99.6	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	392529	392777	ssaI	0/0	100.0	100.0	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	391783	392532	ssaJ	0/0	100.0	99.3	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	390546	391220	ssaK	0/0	100.0	99.6	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	389564	390580	ssaL	0/0	100.0	99.1	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	389138	389506	ssaM	0/0	100.0	99.7	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	385817	387118	ssaN	0/0	100.0	99.5	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	385437	385814	ssaO	0/0	100.0	100.0	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	385082	385456	ssaP	0/0	100.0	99.7	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	384133	385101	ssaQ	0/0	100.0	98.5	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	383418	384065	ssaR	0/0	100.0	98.9	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	383155	383421	ssaS	0/0	100.0	99.6	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	382375	383154	ssaT	0/0	100.0	98.7	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	381320	382378	ssaU	0/0	100.0	99.2	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	387108	389153	ssaV	0/0	100.0	99.5	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	397815	398288	sscA	0/0	100.0	98.9	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	394850	395284	sscB	0/0	100.0	100.0	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	398882	399208	sseA	0/0	100.0	99.7	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	398285	398875	sseB	0/0	100.0	100.0	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	396358	397812	sseC	0/0	100.0	98.1	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	395755	396342	sseD	0/0	100.0	97.5	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	395336	395752	sseE	0/0	100.0	98.8	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	394052	394834	sseF	0/0	100.0	99.4	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	393366	394055	sseG	0/0	100.0	99.3	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	160636	161862	sseJ	0/0	100.0	99.4	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_163059 cov_15.5223	105417	106463	sseK2	0/0	100.0	99.9	NP_461081	(sseK2) type III secretion system effector SseK2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_85728 cov_16.0105	43211	44164	sseL	0/0	100.0	97.6	NP_461229	(sseL) type III secretion system effector SseL deubiquitinase [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_13 length_163059 cov_15.5223	4325	6691	sspH2	0/0	100.0	99.7	NP_461184	(sspH2) type III secretion system effector SspH2 E3 ubiquitin ligase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	213013	213632	steA	2/15	97.8	96.2	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	163133	163534	steB	0/0	100.0	99.8	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_2 length_403085 cov_13.5055	91596	92969	steC	0/0	100.0	99.3	NP_460656	(steC) type III secretion system effector SteC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_37 length_4319 cov_8.69323	849	1770	tcpC	2/2	99.8	95.9	NP_754290	(tcpC) Tir domain containing protein TcpC [TcpC (VF0413)] [Escherichia coli CFT073]

MS0504

Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product
NODE_18 length_67170 cov_16.7038	63841	64748	avrA	1/1	99.9	99.8	NP_461786	(avrA) type III secretion system effector AvrA acetyltransferease [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_60557 cov_16.6091	9435	9977	bcfA	0/0	100.0	99.8	NP_459026	(bcfA) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_60557 cov_16.6091	8648	9334	bcfB	0/0	100.0	99.4	NP_459027	(bcfB) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_60557 cov_16.6091	6022	8643	bcfC	0/0	100.0	99.0	NP_459028	(bcfC) fimbrial usher [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_60557 cov_16.6091	5014	6021	bcfD	0/0	100.0	98.8	NP_459029	(bcfD) fimbrial adhesin protein [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_60557 cov_16.6091	4468	5013	bcfE	0/0	100.0	98.0	NP_459030	(bcfE) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_60557 cov_16.6091	3934	4452	bcfF	0/0	100.0	100.0	NP_459031	(bcfF) fimbrial subunit [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_20 length_60557 cov_16.6091	3237	3968	bcfG	0/0	100.0	98.9	NP_459032	(bcfG) fimbrial chaparone [bovine colonization factor (Bcf) (AI058)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	93875	94330	csgA	0/0	100.0	100.0	NP_460115	(csgA) curlin major subunit CsgA [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	93378	93833	csgB	0/0	100.0	100.0	NP_460114	(csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	94392	94718	csgC	0/0	100.0	100.0	NP_460116	(csgC) curli assembly protein CsgC [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	91973	92623	csgD	0/0	100.0	99.5	NP_460113	(csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	91573	91968	csgE	0/0	100.0	100.0	NP_460112	(csgE) curli production assembly/transport protein CsgE [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	91130	91546	csgF	0/0	100.0	100.0	NP_460111	(csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	90270	91103	csgG	0/0	100.0	99.5	NP_460110	(csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_86138 cov_15.052	9357	10049	fimC	0/0	100.0	99.4	NP_459540	(fimC) chaperone protein FimC [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_86138 cov_15.052	6714	9326	fimD	0/0	100.0	98.7	NP_459541	(fimD) usher protein FimD [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_86138 cov_15.052	5164	5682	fimF	0/0	100.0	98.7	NP_459543	(fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_86138 cov_15.052	5692	6699	fimH	0/0	100.0	98.1	NP_459542	(fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_12 length_86138 cov_15.052	10093	10626	fimI	0/0	100.0	99.4	NP_459539	(fimI) fimbrial protein internal segment [Type 1 fimbriae (VF0102)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	5501	7558	invA	0/0	100.0	99.4	NP_461817	(invA) type III secretion system major export apparatus protein InvA [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	7582	7989	invB	0/0	100.0	99.0	NP_461816	(invB) type III secretion system protein InvB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	7986	9281	invC	0/0	100.0	98.8	NP_461815	(invC) type III secretion system ATPase InvC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	4358	5476	invE	0/0	100.0	99.9	NP_461818	(invE) type III secretion system gatekeeper invE [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	2026	2676	invF	0/0	100.0	99.8	NP_461820	(invF) type III secretion system regulatory protein InvF [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	2673	4361	invG	0/0	100.0	99.2	NP_461819	(invG) type III secretion system secretin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	1127	1570	invH	0/0	100.0	99.3	NP_461821	(invH) type III secretion system pilotin invG [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	9259	9702	invI	0/0	100.0	99.8	NP_461814	(invI) type III secretion system stalk protein InvI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	9702	10712	invJ	0/0	100.0	99.5	NP_461813	(invJ) type III secretion system needle length regulator InvJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_105 length_11850 cov_21.7432	11207	11743	lpfA	0/0	100.0	99.8	NP_462541	(lpfA) long polar fimbria protein LpfA [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_105 length_11850 cov_21.7432	10424	11122	lpfB	0/0	100.0	99.9	NP_462540	(lpfB) long polar fimbrial chaperone protein LpfB [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_105 length_11850 cov_21.7432	7873	10401	lpfC	0/0	100.0	99.7	NP_462539	(lpfC) long polar fimbrial usher protein LpfC [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_105 length_11850 cov_21.7432	6776	7855	lpfD	0/0	100.0	99.9	NP_462538	(lpfD) long polar fimbrial protein LpfD [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_105 length_11850 cov_21.7432	6243	6770	lpfE	0/0	100.0	99.8	NP_462537	(lpfE) long polar fimbrial minor subunit LpfE adhesin [Lpf (VF0105)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_94112 cov_18.4614	49389	52115	mgtB	0/0	100.0	99.2	NP_462662	(mgtB) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_94112 cov_18.4614	48474	49169	mgtC	0/0	100.0	99.0	NP_462663	(mgtC) Mg2+ transport protein [MgtBC (VF0106)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_84 length_19144 cov_15.2427	2840	3736	mig-14	0/0	100.0	98.9	NP_461708	(mig-14) antimicrobial peptide resistance protein Mig-14 [Mig-14 (VF0395)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_9 length_94112 cov_18.4614	56030	58897	misL	0/0	100.0	99.2	NP_462656	(misL) putative autotransporter [MisL (VF0397)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_119 length_6242 cov_14.1665	4446	5045	orgA	0/0	100.0	99.8	NP_461791	(orgA) type III secretion system accessory cytosolic protein OrgA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_119 length_6242 cov_14.1665	5002	5682	orgB	0/0	100.0	99.8	NP_461790	(orgB) type III secretion system stator OrgB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_119 length_6242 cov_14.1665	5679	6131	orgC	0/0	100.0	99.6	NP_461789	(orgC) type III secretion system effector OrgC [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	39244	40119	pipB	0/0	100.0	99.8	NP_460061	(pipB) type III secretion system effector PipB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_84 length_19144 cov_15.2427	47	1099	pipB2	0/0	100.0	98.2	NP_461706	(pipB2) type III secretion system effector PipB3 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_119 length_6242 cov_14.1665	1950	3128	prgH	0/0	100.0	99.2	NP_461795	(prgH) type III secretion system outer MS ring protein PrgH [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_119 length_6242 cov_14.1665	3153	3395	prgI	0/0	100.0	100.0	NP_461794	(prgI) type III secretion system needle filament protein PrgI [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_119 length_6242 cov_14.1665	3414	3719	prgJ	0/0	100.0	100.0	NP_461793	(prgJ) type III secretion system inner rod protein PrgJ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_119 length_6242 cov_14.1665	3716	4474	prgK	0/0	100.0	99.9	NP_461792	(prgK) type III secretion system inner MS ring protein PrgK [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_95 length_16729 cov_16.0467	9191	16498	ratB	2/6	100.0	98.7	NP_461449	(ratB) putative outer membrane protein [RatB (VF0399)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	14563	15060	sicA	0/0	100.0	99.8	NP_461807	(sicA) chaparone for SipC and SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	21877	22269	sicP	0/0	100.0	99.2	NP_461800	(sicP) chaparone for SptP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	172083	173093	sifA	0/0	100.0	100.0	NP_460194	(sifA) type III secretion system effector SifA N-terminal SKIP-binding domain C-terminal guanine nucleotide exchange factor activity [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_94 length_16950 cov_12.0072	15928	16878	sifB	0/0	100.0	99.5	NP_460561	(sifB) type III secretion system effector SifB [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_95 length_16729 cov_16.0467	96	2288	sinH	0/0	100.0	99.5	NP_461452	(sinH) intimin-like protein [SinH (VF0400)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	19222	21279	sipA/sspA	0/0	100.0	99.8	NP_461803	(sipA/sspA) type III secretion system effector SipA actin polymerizing activity [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	15063	16844	sipB/sspB	0/0	100.0	99.2	NP_461806	(sipB/sspB) type III secretion system hydrophilic translocator pore protein SipB [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	16872	18101	sipC/sspC	0/0	100.0	99.6	NP_461805	(sipC/sspC) type III secretion system hydrophilic translocator pore protein SipC [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	18172	19203	sipD	0/0	100.0	99.8	NP_461804	(sipD) type III secretion system hydrophilic translocator needle tip protein SipD [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_11 length_88493 cov_13.4831	28859	31126	slrP	2/30	98.7	96.8	NP_459778	(slrP) type III secretion system effector SlrP E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_34 length_45637 cov_15.5388	24884	27232	sopA	0/0	100.0	99.2	NP_461011	(sopA) type III secretion system effector SopA E3 ubiquitin ligase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_1 length_206809 cov_13.4863	41025	42710	sopB/sigD	0/0	100.0	99.8	NP_460064	(sopB/sigD) type III secretion system effector SopB phosphoinositide phosphatase [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_58 length_28598 cov_11.9214	12286	13008	sopE2	0/0	100.0	99.9	NP_460811	(sopE2) type III secretion system effector SopE2 guanine nucleotide exchange factor [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	10712	11623	spaO	0/0	100.0	99.1	NP_461812	(spaO) type III secretion system C ring protein SpaO [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	11613	12287	spaP	0/0	100.0	99.8	NP_461811	(spaP) type III secretion system minor export apparatus protein SpaP [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	12313	12573	spaQ	0/0	100.0	100.0	NP_461810	(spaQ) type III secretion system minor export apparatus protein SpaQ [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	12577	13368	spaR	0/0	100.0	99.4	NP_461809	(spaR) type III secretion system minor export apparatus protein SpaR [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	13355	14425	spaS	0/0	100.0	99.8	NP_461808	(spaS) type III secretion system export apparatus switch protein SpaS [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	134529	134930	spiC/ssaB	0/0	100.0	100.0	NP_460358	(spiC/ssaB) type III secretion system protein SsaB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_67 length_26468 cov_15.5366	22256	23887	sptP	0/0	100.0	99.8	NP_461799	(sptP) type III secretion system effector SptP tyrosine phosphatase and GTPase-activating protein [TTSS(SPI-1 encode) (VF0116)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	133034	134527	ssaC	0/0	100.0	99.0	NP_460359	(ssaC) type III secretion system secretin SsaC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	131842	133053	ssaD	0/0	100.0	99.2	NP_460360	(ssaD) type III secretion system outer MS ring protein SsaD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	131592	131834	ssaE	0/0	100.0	100.0	NP_460361	(ssaE) chaperone for sseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	125178	125393	ssaG	0/0	100.0	100.0	NP_460371	(ssaG) type III secretion system needle filament protein SsaG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	124910	125137	ssaH	0/0	100.0	100.0	NP_460372	(ssaH) type III secretion system protein SsaH [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	124650	124898	ssaI	0/0	100.0	99.6	NP_460373	(ssaI) type III secretion system inner rod protein SsaI [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	123904	124653	ssaJ	0/0	100.0	99.2	NP_460374	(ssaJ) type III secretion system inner MS ring protein SsaJ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	122667	123341	ssaK	0/0	100.0	99.6	NP_460376	(ssaK) type III secretion system stator SsaK [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	121685	122701	ssaL	0/0	100.0	99.1	NP_460377	(ssaL) type III secretion system gatekeeper SsaL [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	121259	121627	ssaM	0/0	100.0	100.0	NP_460378	(ssaM) type III secretion system protein SsaM [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	117938	119239	ssaN	0/0	100.0	98.8	NP_460380	(ssaN) type III secretion system ATPase SsaN [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	117558	117935	ssaO	0/0	100.0	99.7	NP_460381	(ssaO) type III secretion system stalk protein SsaO [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	117203	117577	ssaP	0/0	100.0	99.5	NP_460382	(ssaP) type III secretion system needle length regulator SsaP [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	116254	117222	ssaQ	0/0	100.0	98.1	NP_460383	(ssaQ) type III secretion system C ring protein SsaQ [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	115539	116186	ssaR	0/0	100.0	98.9	NP_460384	(ssaR) type III secretion system minor export apparatus protein SsaR [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	115276	115542	ssaS	0/0	100.0	99.6	NP_460385	(ssaS) type III secretion system minor export apparatus protein SsaS [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	114496	115275	ssaT	0/0	100.0	98.5	NP_460386	(ssaT) type III secretion system minor export apparatus protein SsaT [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	113441	114499	ssaU	0/0	100.0	99.0	NP_460387	(ssaU) type III secretion system export apparatus switch protein SsaU [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	119229	121274	ssaV	0/0	100.0	99.8	NP_460379	(ssaV) type III secretion system major export apparatus protein ssaV [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	129936	130409	sscA	0/0	100.0	98.7	NP_460364	(sscA) chaperone for sseC [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	126971	127405	sscB	0/0	100.0	100.0	NP_460368	(sscB) chaperone for sseF [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	131003	131329	sseA	0/0	100.0	99.7	NP_460362	(sseA) chaperone for sseB and sseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	130406	130996	sseB	0/0	100.0	99.8	NP_460363	(sseB) type III secretion system effector SseB [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	128479	129933	sseC	0/0	100.0	99.0	NP_460365	(sseC) type III secretion system hydrophilic translocator pore protein SseC [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	127876	128463	sseD	0/0	100.0	100.0	NP_460366	(sseD) type III secretion system hydrophilic translocator pore protein SseD [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	127457	127873	sseE	0/0	100.0	100.0	NP_460367	(sseE) type III secretion system effector SseE [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	126173	126955	sseF	0/0	100.0	99.4	NP_460369	(sseF) type III secretion system effector SseF [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_3 length_135045 cov_13.5288	125487	126176	sseG	0/0	100.0	99.6	NP_460370	(sseG) type III secretion system effector SseG [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_111 length_7838 cov_10.2377	6169	7395	sseJ	0/0	100.0	99.4	NP_460590	(sseJ) type III secretion system effector SseJ glycerophospholipid:cholesterol acyltransferase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_14 length_77860 cov_15.3187	48441	49487	sseK2	0/0	100.0	99.7	NP_461081	(sseK2) type III secretion system effector SseK2 [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_22 length_59219 cov_14.7691	42936	43889	sseL	0/0	100.0	97.7	NP_461229	(sseL) type III secretion system effector SseL deubiquitinase [SPI-2 encoded T3SS (SS021)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_101 length_13335 cov_11.1965	3486	5597	sspH1	1/9	100.0	97.9	AAD40326	(sspH1) type III secretion system effector SspH1 E3 ubiquitin ligase [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s]
NODE_63 length_26799 cov_14.3557	2951	5317	sspH2	0/0	100.0	99.7	NP_461184	(sspH2) type III secretion system effector SspH2 E3 ubiquitin ligase [TTSS(SPI-2 encode) (VF0321)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_79 length_21202 cov_12.2853	6157	6789	steA	0/0	100.0	98.4	NP_460542	(steA) type III secretion system effector SteA [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
NODE_62 length_27019 cov_12.7387	26366	26767	steB	0/0	100.0	100.0	AAL20547	(steB) type III secretion system effector SteB [SPI-1 encoded T3SS (SS010)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]

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Plasmids

The search of plasmid replicons was performed by screening of the draft genome against PlasmidFinder database (A. Carattoli et al., 2014) by using Abricate. Any hit with coverage and/or identity below 90% was removed. To see description of each field, click here.

Select the sample

MS0495

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0496

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0497

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0498

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0499

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0500

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0501

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0502

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0503

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

MS0504

## [1] "No plasmid replicon genes from Plasmidfinder database were found"

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Citation

TORMES has already been submitted to publication. If using TORMES before publication is released, please cite as:

Quijada, N.M., Rodríguez-Lázaro, D., Hernández, M. TORMES. (2018) GitHub (https://github.com/nmquijada/tormes/)

Also cite the software and databases that are included in TORMES pipeline:

• Abricate, T. Seemann
• ARG-ANNOT Database, S.K. Gupta et al., 2014
• BLAST, Z. Zhang et al., 2000
• The Comprehensive Antibiotic Resistance Database (CARD), A.G. McArthur et al., 2013
• FastTree, M.N. Price et al., 2009
• Kraken, D.E. Wood and S.L. Salzberg, 2014
• progressiveMauve. A.E. Darling et al., 2010
• mlst, T. Seemann
• Parallel, O. Tange, 2011
• Prinseq, R. Schmieder and R. Edwards, 2011
• Prokka, T. Seemann, 2014
• QUAST, A. Gurevich et al., 2013
• R, R Development Core Team, 2008
  • ggplot2, H. Wickham, 2009
  • ggtree, G. Yu et al., 2016
  • knitr, Y. Xie, 2015
  • plotly, C. Sievert et al., 2017
  • RColorBrewer, E. Neuwirth and R.C. Brewer, 2014
  • reshape2, H. Wickham, 2007
  • rmarkdown, J.J. Allaire, 2015
• Roary, A.J. Page et al., 2015
• roary2svg, T. Seemann
• ResFinder Database, E. Zankari et al., 2012
• SPAdes, A. Bankevich et al., 2012
• Trimmomatic, A.M. Bolger et al., 2014
• Virulence Factors Database (VFDB), L. Chen et al., 2005

Software and databases used for special analyisis enabled by -g/--genera Salmonella option:

• PlasmidFinder Database, A. Carattoli et al., 2014
• PointFinder, E. Zankari et al., 2017
• SISTR C.E. Yoshida et al., 2016